Bioshock/WMG

Bioshock takes place in the Magic: The Gathering multiverse
Because, let's face it, it's an extreme coincidence that the two big bads represent the worst of Black and White. Meanwhile, the sea slugs that make ADAM have something to do with Phyrexia.

"No Please" is the automatic response no "Would You Kindly."

 * We just don't hear it because Jack is supposed to be a Heroic Mime. Remember in the audio log? Of course Jack didn't want to kill the puppy, but think about it; how did Fontaine immediately know that Jack disobayed him? He didn't say the code phrase back.

Andrew Ryan is Quark from Star Trek: Deep Space Nine
Quark has visited 20th century Earth before. He wouldn't have a very difficult time returning, as time travel is a fairly regular occurrence in Star Trek. As for his motives, remember that his brother Rom became Nagus and the Ferengi were already undertaking a number of reforms to their society. Rom would probably continue on this course and make Ferengi society more like the Federation way of life, and strengthen relations with the Federation. After all, he was specifically selected by Zek because he wasn't a traditional profit-centric Ferengi like Quark. Consider the effect this would have on Quark; he would watch in horror as his own brother destroyed everything about Ferengi society that Quark had believed in and built his life around. So, Quark decided to get revenge on humanity by trying to ensure that humanity never abandoned capitalism.

Now, I realize this would be massive character derailment, but consider that other Ferengi depicted in the series have been shown to be quite vicious, vindictive, and completely amoral when isolated from their society e.g. many TNG Ferengi and the space pirate Ferengi in Enterprise. Although this has never been formally addressed in canon, it would seem that Ferengi go insane when cut off from the comforts of their capitalistic culture. Since as far as Quark was concerned, his culture was destroyed forever, he would probably have gone completely insane. His only motive at that point was payback against those who tore down his culture, the human race.

First, he would have to be able to live among humans unnoticed. Given Quark's extensive black market connections, he wouldn't have difficult time finding someone who could perform the necessary genetic and surgical alterations to disguise him. Then he acquired whatever advanced technology he could get his hands on to take to 20th century Earth in an attempt to revolutionize human society in a way that would ensure that they would continue to support capitalism in the centuries that followed. This included advanced genetic engineering technology that could grant the empathic and telekinetic abilities seen in some species to humans. This technology became the basis for the radical genetic alterations seen in the Splicers. In addition, he brought other advanced tech that would make it possible to build an underwater city with computerized security and defense systems.

Because time travel can be dangerous and unpredictable, he was unable to control exactly which time he could travel to, so let's say he was targeting sometime in the late 19th-early 20th century when collectivist movements began gaining momentum. Now, his actual trip back in time didn't go as planned, and he ended up with much of the advanced tech he brought back damaged, but enough of it survived that he was able to use his own knowledge of it's working to recreate it with early 20th century equipment and materials. He wasn't able to prevent the Russian Revolution of 1917, but he was able to establish an objectivist movement which then laid the foundation for Rapture. His human name was intentionally chosen based on Ayn Rand's name and her works were the inspiration for his vision for humanity's future. His goal at that point was to set up a free market society which would be able to survive a nuclear war, and then goad the USA and Soviet Union into destroying each other. Obviously, he no longer had 24th century weapons available, or he would have been able to wipe out the USA and USSR on his own. Unfortunately, this meant that he wouldn't be able to fully isolate Rapture from the influences of the surface world, otherwise he would be unable to manipulate the surface powers into engaging in nuclear war.

It was his attempts to infiltrate the US and Soviet governments that left Rapture vulnerable. OSS caught wind of his operation and assisted mafia backed smugglers in their business of providing contraband goods to the citizens of Rapture. This is what led to Fontaine's rise to power and the eventual conflict the caused the collapse of Rapture's society.

Rapture is not located underwater; the views from the bathysphere and from the observation windows are elaborate tricks used to dazzle a casual observer.
If it had been underwater, it is doubtful that whales and giant squid would swim so close or that the building exteriors would be free of your typical underwater growths. Also, there is no evidence of the adverse effects of being underwater (air pressure and so on) affecting the residents. All of the water leaking in all over the place is part of the illusion.
 * No, the water that "leaks" in is real--it's piped in from somewhere to form "leaks" to enhance the illusion of there being water outside. It's not illusory water.
 * The effects of living underwater could have been major problems for the people living in Rapture before everyone went crazy; they're just too far gone by now for it to be noticeable. The people living in Rapture didn't go psychotic long before the start of the game, either, so they could have been removing plant life and barnacles from their buildings up until a few years before the main character arrives in the city.
 * Debunked in Bioshock 2. You play as the first Big Daddy and there are scenes in which you can walk on the ocean floor.
 * However, you're encased in a huge suit of powered armor, with only a little window into the world. If the conspirators can project images into every window in Rapture, surely they can do the same to your helmet's visor! (Yeah, yeah, and we might all be brains in jars, I know.)
 * Still Jossed by the ending. You can physically see the ocean from the cutscene outside the ballast escape pod.
 * Err, what about the fact that you're swimming in the goddamn ocean at the beginning of the first game? Then you step into the lighthouse, and go to the bathysphere. Therefore, you are definitely underwater. In fact, you're already underwater when you enter the bathysphere, albeit, not too far. And don't you dare say it was All Just a Dream.
 * Rapture was just a hallucination caused by an Android trying to drown you in an aquarium, really it is 1912 and you're in a flying city. http://pc.ign.com/dor/objects/14258733/bioshock-3/videos/bioshock_trl_081210.html?show=hi
 * Also Jossed. Word of God says that Bioshock Infinites Colombia (the flying city) is set in the same universe as Rapture.
 * Same universe, maybe, but Word of God also says its a different timeline.

Rapture IS underwater, and close to R'lyeh.
Back in the 40's, when Rapture was constructed, DNA testing wasn't mainstream, let alone DNA modification. The injections that rewrite your DNA to let you shoot lightning (in an underwater city) are just Lovecraftian magic combined with the side effects of being anywhere near Cthulhu. Big Daddies are Deep Ones (Bouncer), and those with the Innsmouth taint (Rosie) magically bound into service by Andrew Ryan. Fontaine didn't want Rapture; he wanted the Necronomicon, the thing that allowed Ryan to build an entire city at the bottom of the ocean.
 * Which leads to some interesting speculation regarding after he becomes a Big Daddy.
 * Well, Gil Alexander's mutated form does look an awful lot like Cthulhu.

Rapture isn't near Ry'leh, but it IS in a Lovecraftian universe
The universe created by Lovecraft encompasses far more then just the usual suspects like Ry'leh, Cthulhu and the Deep Ones. However, the existance of strange slugs who's extracts allow for genetic manipulations beyond the logical possibilities of human DNA does sound strangely Lovecraftian. Especially since their introduction to Rapture inevitably leads to Madness taking over the populace. Those slugs were indeed Things Man Was Not Meant to Know... ""God is sleeping Mr. B, in the water. Wait 'n see.""
 * Possibly confirmed by the viral website for the sequel - one of the pieces of paper says that
 * This troper agrees with this theory, and would like to make an addition. The ADAM slugs are the gibletized remains of a Eldritch Abomination. after all,
 * Also, one of the idle Little Sister quotes in Bioschock 2 (when she's with another Big Daddy, to be precise) is;


 * Which is a pretty obvious reference to Cthulhu. This is also relevant to the previous WMG.

The Big Daddies act as Rapture's Maintenance crew
In the initial descent to Rapture, we see a Big-Daddy-sized creature repairing one of the tunnels. Additionally, while Splicers get much less common as areas are cleaned out, there is always a fixed number of Big Daddies in any given area, meaning that they're coming in from somewhere. There's also the fact that they're wearing giant, self-contained diving suits. When an individual Big Daddy isn't defending a Little Sister, he's making repairs or removing underwater growths from the outside of Rapture's various buildings.
 * There is actually substantive evidence suggesting this. The two primary BD weapons? A giant drill (useful for cleaning off the outside of Rapture), and a rivet gun, which could be used to patch leaks. Not to mention that, in at least 1 area of Rapture, you can see dead Big Daddies sitting on the ocean floor, OUTSIDE of Rapture. Now what are they doing out there?
 * We aren't looking at this closely enough; the Big Daddies aren't who the equipment was designed for. It started out as maintenance equipment, and was co-opted by the Bigs, who are sick fucking bastards, by the way, to help them "protect" the innocent girls that they mind control and turn into ADAM processors. Like a lot of horrible things, this wasn't part of the plan originally, but became institutionalized when it went out of control. Which is why we see infrastructure dedicated to Big Daddies and Little Sisters.
 * More accurately, it was co-opted by the people who created the Big Daddies and Little Sisters, who are most certainly sick fucking bastards. The Big Daddies themselves are more or less mindless automata.
 * Pretty much confirmed in the beginning stage of Bioshock 2, where a Rosie is clearly seen repairing a leak from the outside. Keep in mind this takes place some ten odd years after Rapture went to hell in a hand basket.
 * One fanfic suggested an explanation: whenever the Big Daddies see a leak, they obsess over the danger it presents to the Little Sisters, who can still drown.

Andrew Ryan is still alive.
In Ryan's office is a Vita-chamber, sealed up but apparently functional. The Vita-chambers work based on Ryan's DNA. Not a big leap to think he cloned himself after you left and escaped/went after Fontaine/is building a new Rapture/etc.
 * Except that if you examine it you'll discover that that Vita-Chamber was specifically shut off (the only such in the game). Ryan intentionally let himself die, on his own terms, in hopes that this display of Jack's lack of free will would cause him to rebel against and kill Atlas/Fontaine. Also, there's the whole "betraying everything he stands for" thing, which may've grown too much for him.
 * If you listen to one of his last radio messages, he says 'Now that I have seen you, know that I cannot fight you...' Given the twist that happens RIGHT AFTER THAT, he did it because he couldn't bear to kill his own child. He knew he couldn't manipulate Jack for long, and that Atlas had the upper hand, and he chose to die forever rather than shoot his own son.
 * In retrospect, the Vita Chamber's instructions say that he will be cloned at the NEAREST AVAILABLE CHAMBER. What's to say that Ryan didn't decant at another chamber (the chamber just outside of Ryan's office, if I recall) and flee Rapture?
 * I've perused some of the plot guides from Gamefaqs, and supposedly Vita Chambers don't work that way. It seems there aren't any of the chambers near Suchong's apartment, so if you die there, you get a game over instead of a regeneration. Also keep in mind that Ryan had access to bathyspheres and other subs - if he wanted to leave Rapture, he had ample opportunity to do so.
 * The same applies to the final boss, you get a message stating that you cannot save and there are no vita chambers nearby, so if you die you have to start over from the autosave.
 * There's one near enough to Ryan's office though. If you die in Ryan's office, you pop out at the Chamber near the Bathysphere. Also, who says he wanted to leave? Ryan still believes Rapture can be saved. He wanted to manipulate the player into killing off Fontaine, leaving him with no genuine opposition.
 * Look at it this way--the sequel has to have a villain, and Sander Cohen probably isn't up for it. That leaves either Ryan, or you in the evil ending, and while the latter would be a cooler twist, developers seem curiously squeamish about making evil paths canonical.
 * Jossed by the previews; Big Sister is quite clearly the villain. There may very well be a twist about her role, but Ryan isn't necessary as an opposing force.
 * It doesn't say that he's not alive...just that he's not * the* villain. Though it would completely wreck the scene of his death in Bioshock considering how he went out of his way to make his death a giant Mind Screw for Jack. Also, Big Sister runs Rapture now, so if he were alive, he apparently has no power over the city anymore.
 * Actually, a recent issue of Gamepro states that the Big Sister is a villain; just not the main villain. She is most likely going to play the part of muscle and act as his/her enforcer. Who, then, is the main villain? Personally, this troper has his money on someone we've met before (though he has no idea who that might be, since most of the characters from the first game, are, you know, out of commission...)
 * News these days seem to say that the main baddie of Bioshock 2 is some sort of cult leader that the Splicers and Big Sisters follow who wants to kill you and bring Rapture back to its former state.
 * I could imagine him singing Still Alive.
 * Oh god, now I can't get Ryan singing that out of my head. Thanks.
 * Even if he did die 'for good', Bioshock 2's resurrection of Delta 10 years after he died proves that Vita-Chambers do not have to be used immediately. Ryan could have paid off a Splicer or convinced a Little Sister or something to revive him after the situation in Rapture had calmed down.

The Big Daddies are actual fathers
Its never mentioned who they actually are, only that recruits will be easy to find. Since they had a lot of difficulty getting Big Daddies to like the little sisters, they may have tried using men who already have young daughters, since they would be more receptive to being around (and protecting) young girls. Part of the Big Daddy creation process would then include a plasmid that tricks them into believing that all of the little sisters are in fact their own children, which can explain their intense devotion towards protecting them.
 * This theory could make sense, as in the sequel you see the Little Sisters in a cleaner and more sympathetic light, you yourself being a Big Daddy.
 * Except that, in one instance, you see a couple who committed suicide after seeing their daughter as a Little Sister.
 * That doesn't mean anything, except for the husband in that particular family wasn't chosen to be a Big Daddy. With the above theory that plasmids make each Big Daddy believe each Little Sister is his own daughter, you wouldn't need to nab both the father and the child from the same family.
 * Its also shown in the factory that creates the little sisters that the Big Daddies get their food when the sister gives out her Adam. There's a button marked with a little sister symbol, and a big daddy symbol. The sister button gets you hurt (Symbolizing that A needle just jabbed you) and then when you activate the Big Daddy Button, Chip bags fall out. Note however: You cannot simply push the big daddy button over and over, You have to activate the little sister button, and THEN you can get the bag of chips. Being told "Keep this brat safe or you'll starve to death." Is another way to keep them on their toes regarding others in Rapture.
 * Actually, the buttons are labeled with a Big Daddy and standard representation of a man (or a woman, I don't recall which). This area is for training the Little Sisters to associate Big Daddies with reward (hence the chips), and anyone else with punishment/pain (hence the, well, pain). If you look, both buttons are at an inconvenient height for an adult, put perfectly placed for a child.
 * The big daddy button will also re-dispense chips, it just takes a little time to reset. I'd been blown up a lot by the rocket turrets and was out of first aid kits at the time, ducked into that room to get out of sight of the splicers, and I frobbed the button until it barfed up enough chips for me to completely heal. After zapping myself with the other one when the big daddy didn't drop chips the second time...
 * I always assumed that the Big Daddies were Fontaine loyalists or other people Ryan didn't like. Andrew Ryan is not kind to his enemies.
 * Many inmates of Persephone were apparently turned into Big Daddies.
 * Bioshock 2 gives credence to this theory in the form of Mark Meltzer, who came to Rapture specifically to rescue his daughter, who had been turned into a Little Sister. He was arrested for trespassing, and he was given a choice: to be executed, or to become a Big Daddy bonded to his daughter. Upon killing him (unknowingly, as when you meet him he seems to be just another Big Daddy - but his corpse is labeled), his daughter reacts the same as every other Little Sister; crying over their dead Daddy at first, and then accepting the player as their new Daddy, completely forgetting their former one. You gotta feel for the guy, after all he went through to get her back.

Fontaine is still alive
We saw the little sisters stab the hell out of him...but that doesn't mean a giant plasmid mutant like he became is necessarily dead. The red glow under the ocean and the kidnappings of the young girls are all Fontaine trying to get more ADAM sources again. In the good canon, Jack took all the Little Sisters with him, so Fontaine is trying to find them and starts snatching little girls of the right age assuming they could be the same.
 * The teaser trailer shows what appears to be an older Little Sister holding a Big Daddy doll. The doll is still on the site. Two of the kidnapped girls have the same last name - one with a family, one from an orphanage. They all look very similar too.
 * According to Game Informer, Fontaine Futuristics will be visited, especially the place where the ADAM is processed from the Little Sisters. Doesn't mean he's alive, the Big Sister could have easily gotten it running herself, but even so, it's there.
 * As a alternative method of survival, he could have used the vita chambers. He knows they exist and work, he has the genetic key to Rapture, and seemed to have a back up plan for everything. It's not hard to imagine that he attuned them to his genetic code while he was preparing for his battle with Jack. Having them used against you in the second game would be a nice twist on things.

The bad ending is canon
The alternative to the above -  The red glow under the sea is a   preparing his invasion of the surface world.
 * The latest updates discuss the potential of the glow being a submarine. Dun dun DUN!
 * It's a Big Sister running the sub.
 * Jossed. The plot of Bioshock 2 only works assuming Jack didn't destroy/take over the world in the seven year gap between the games. Plus, Jack is no longer present in Rapture in the second game.

Combining two of the above WMGs, the Big Bad of Bioshock 2 will be none other than
Since we know that Big Sister isn't the main villain, someone has to be. And if the bad ending is canon, then  Here's my guess. After leaving for some time, he returned to Rapture, bringing a Little Sister with him. He forced her to become the Big Sister and perhaps controls her from afar. He is capturing girls to make into new Little Sisters because he wants to see Rapture rebuilt the way it was : brimming with ADAM.
 * Jossed. The main villain of Bioshock 2 is Sofia Lamb.
 * Perhaps in Infinite, than. Wait, that's a prequel! Damn.

Tennenbaum is the Big Sister
Whoever it is fanatically protective of the little sisters to the point of kidnapping at least a dozen little girls to convert into the little girls. Tennenbaum notes in her audio logs how obsessive her maternal instinct is, and what other major player is left in the city after the end of the game?
 * Promotional material seems to indicate that the Big Sister is a lost Little Sister that Jack and Tennenbaum never encountered during their stay in Rapture.
 * Further Jossed - GameInformer shows her alive in 1967. She apparently escaped with a group of Little Sisters (regardless of what Jack did in the first game). The Big Sister is one of these girls that returned to Rapture and started it up again.
 * Even further Jossed; not only does Tennenbaum show up (albeit not for very long at all), but Big Sisters are generic enemies descended from grown-up Little Sisters, not a single entity.
 * This logic is flawed anyway - Tenenbaum states that she greatly regrets turning the girls into Little Sisters in the first place, so she's not going to go and make more.

The Big Sister is Samus Aran.
Mostly because this page needs more 'fun' theories.
 * She is the prototype for the Power Suit.
 * Unfortunately, there are multiple Big Sisters which kinda puts a dent in this theory.
 * She could be one of several Big Sisters...

Sander Cohen is a series of clones, and will be making a return in Bioshock 2
If you look closely, all of the dead splicers in Cohen's Quadtych are... Sander Cohen himself! There's also a dead Sander Cohen in the "I want to take the ears off!" dressing room. Also, if you kill Cohen in Olympus Heights, then go back to Fort Frolic and trash his Quadtych, he'll appear (apparently back from the dead) to fight you.
 * Maybe as a favor to his old friend, Ryan programmed the Vita-Chambers to resurrect Cohen too? But he's not enough of a raving lunatic to keep attacking you over and over after you kill him the first time?

This may all simply be a series of programming oversights, but the writers could use it as a plot point to bring Cohen back in the sequel. They could even throw in a reference to The Prestige.
 * Jossed. Cohen makes no appearance in the sequel.
 * No physical appearance - try harvesting the two ADAM corpses in Cohen's Collection in the drowned park. Cohen's signature piano piece starts blaring on the speakers, and he laughs and applauds your slaughter of splicers over the speakers once both harvests are done. More of an easter egg, yes, but he's still around.

Demitosse will be a major antagonist in Bioshock 2
If you look out many of the windows in Rapture, you'll see a series of billboards with three names: RYAN, FONTAINE, DEMITOSSE. Since Ryan --> Fontaine was the Big Bad progression in the original game, this has fueled fan speculation that a further Fontaine --> Demitosse plot progression would appear in the sequel, with Demitosse being the new Big Bad.
 * It's actually spelt Demitasse. According to The Other Wiki a demitasse is a small coffee or tea cup and, considering the text under "demitasse" in the screenshot, it's probably just an ad for tea or tea cups rather than the name of some mysterious Big Bad.
 * So the next Big Bad will be a cup of Coffee... Oh my god... Homsar's Father!
 * Jossed, since there hasn't been any mention of a Demitosse anywhere in the game.

The Big Sister will be killed about halfway through the game, plunging Rapture into chaos. The rest of the game will be spent trying to fix the mess.
The promo material for Bioshock 2 makes a considerable deal about how the Big Sister's influence has resulted in Rapture reaching a state of stability/equilibrium. Yet, seeing as how she's kidnapping girls from the surface and also apparently trying to kill you, it's pretty obvious we're expected to hunt her down. This will ultimately lead to a plot twist similar to the original Bioshock where killing the apparent Big Bad only makes things worse.

It's possible that the game's real Big Bad will manipulate the player into killing the Big Sister before revealing themselves. However, this is a bit too similar to the original game's big plot twist to expect that they'd use it again. The player may simply kill the Big Sister because, well, that's what players do, and thus unlike Jack will be fully morally responsible for the act and the resulting chaos.
 * Jossed; there are multiple Big Sisters and none of them seem to be anything more than enforcers.

The Big Sister is the former Little Sister of the first Big Daddy.
The April '09 issue of Game Informer states that the player-character of Bioshock 2 will not only be a Big Daddy, he'll be the first Big Daddy. It's possible that the Big Sister is one of the rescued Little Sisters who couldn't fully escape her conditioning. Returning to Rapture, she's determined to regain her earlier life by becoming a Big Daddy (well, Big Sister) to the other girls, who she assumes also misses Rapture as much as she did. This matters because at some point during the game, your identity as the first Big Daddy will matter... because before Jack separated the two of you, Big Sister was your Little Sister, and therefore the first Little Sister herself.
 * You know the tape when Dr. Suchong slaps a little sister and killed by the big daddy he was working on? That's Big Sister and the first Big Daddy
 * To add to this theory, after a certain point in the game, probably as a good ending path, after the player defeats Big Sister for good and a new threat shows up, Big Sister and the player will have to team up to stop the new bad guys. However, as a result of their fight Big Sister will be barely able to walk and will have to ride on the player's back, reflecting their previous Big Daddy-Little Sister relationship.
 * Jossed; there are multiple Big Sisters, and the original Little Sister of Subject Delta has not yet been converted into a Big Sister as Lamb has plans for her.
 * Eleanor does become a Big Sister near the end of the game, though.

The girl in the Bioshock 2 trailer is Big Sister
She's obviously an older Little Sister and I think it's safe to assume she misses at least part of Rapture as she still owns a (homemade) Big Daddy doll and it watching the sea. The rising city in the sand could represent her return to Rapture, where she outfits herself with the Big Sister suit. As for her motive, I'm not quiet sure... Maybe she thinks being a Little Sister was awesome and wants to make other girls experiance what she did? I don't know.
 * Jossed; a case of Never Trust a Trailer.

The Big Sister will go after Tenenbaum and Jack once she has collected enough Little Sisters.
Her ultimate goal is to assemble some kind of creepy version of a 'family' to help her rule over Rapture. With Tenenbaum having originally created the Little Sister process, and Jack both having protected them and been in a Big Daddy suit at one point, they will be her parental figures.
 * Jossed; there is no one Big Sister, since they're generic.

Andrew Ryan was working on a rudimentary AI construct.
In part because someone else hinted at it in the main page, in part because I've been thinking of it since I first played the game. The Big Sister form is dead, insect!
 * Confirmed as of Minerva's den. Thankfully, AI Is a Crapshoot is averted.

The Big Sister is an Emo Teen.
A recent interview claims that the Big Sister was once a Little Sisters who went up to the surface, but came back down years later for some reason. The whole "kidnapping children and becoming a supervillain" thing is a cry for attention from her adopted family. Which may or may not be Jack.
 * "I don't care what the other kids at school are doing. As long as live under my roof, you are not getting Big Daddy enhancements!"
 * While amusing, Jossed.

The second game will include some kind of fight against an underwater creature.
Sure, they tell us that the water-walk sections will be a break to survey our surroundings, but it's all just a clever set up to make us wet our pants when some kind of giant beast comes at us through the murky depths. Maybe a shark or an octopus exposed to the ADAM (either accidentally or by the proposed villain behind the Little Sister), or...a giant queen-type figure of the sea slugs who produce it in the first place? Why, you ask? Because it would be AWESOME.
 * Also, when they say "you can't use weapons underwater," they mean "you can't use any non-Big Daddy weapons underwater."
 * Related to the mention of Innsmouth at the top of the page, it could be some sort of minor Deep One.
 * Jossed. There is no undersea battle of any kind.
 * Well, technically, all of the fights are 'undersea battles'...
 * There is an undersea creature. Gil Alexander apparently escapes into the ocean if you spare him, and if you look at a certain peace of concept art, he's basically bright red Cthulhu.

After the Big Sister is defeated, the player will have to deal with The Government.
The Big Sister is dead. The first Big Daddy has finished his charge and maybe helped Tenenbaum absolve her guilt over being involved with the chaotic downfall of Rapture or something. BUT THEN! Either after ignoring the issue of the mysterious red lights or secretly following it all along, the feds show up and one of them is awed by what could be achieved with the ADAM: science, world conquest, what have you. They could mutiny or bait their entire team into it and try to subdue the Big Daddy before taking their findings above surface. After this transpires, you'll need to help Tenenbaum destroy Rapture once and for all, so the horrible secrets it held are destroyed.
 * Alternatively, you'll end up having to do roughly the same thing, but against The Mafia. Fontaine's old contacts, perhaps?
 * OR EVEN! A former member of Those Wacky Nazis who was jealous of that 'inferior Kraut' Tenenbaum stealing their spotlight?
 * There was the talk of Russia invading Rapture early in development - whether or not they survived the current version of the game is yet to be seen.
 * Jossed. The main villain for the entire game is Sofia Lamb.

Bioshock shares the same universe as Metal Gear.

 * Portable Ops establishes the basis for Big Boss's cloning into Solid, Liquid and Solidus Snakes. This is in the late 1960s. Surely an expert understanding of DNA had to come from somewhere. In Rapture scientists can mutate DNA so that Jack can shoot FIRE out of his hands, showing that expert understanding. Now, if Fontaine's forces smuggled Bibles from outside Rapture, surely it wouldn't be too difficult for a couple of Rapture scientists to come up with the Plasmid technology, smuggle it out and sold their secrets to the US or the Soviet Union. Also to note is the stress on both game series on megascale mechanical engineering. Who knows - scientists who sneaked out from Rapture earlier could have gone to the Soviet Union and incorporate that drill idea for a giant ICBM tank...
 * Thinking about this, a few of the characters in Metal Gear could have their abilities explained by features of Bioshock. MGS3 for example: Volgin has an electroshock plasmid, The Sorrow can see ghosts through ADAM exposure, The Pain uses an insect swarm plasmid, The Fear is a spider splicer with a natural camouflage gene tonic, The Fury is a modified Big Daddy...

Jack is Mister Rogers
He wears a sweater (a bloodstained sweater), puts himself in danger to rescue little girls from a life of terror, and witnessed a truly terrible place where people are treated as objects and either killed or turned into monsters. Its pretty obvious that after his experience in Rapture he would have to give some thought as to how to properly raise the Little Sisters and how society can avoid having another Rapture happen. So he took on the name of Mister Rogers and worked to teach children how to be good neighbors. However, while his new life is dedicated to peace and understanding, he's still every bit of a badass he was in Rapture. That is why he always wins in the Ultimate Showdown of Ultimate Destiny.
 * This is awesome and is now officially canon for both the game and reality.
 * Agreed. To the troper who made this WMG (whose name has, sadly, disappeared from the edit history), I award you a TV Tropes Made of Win Archive.
 * To my knowledge, they're trying to make it so either ending could work, like in Metal Gear Solid 2. Also, didn't Jack get his vocal cords drilled out? Don't get me wrong, I think this is the best theory ever, but I'm 80% certain he didn't get them back.
 * Well, IRL Mister Rogers was a minister, if I remember correctly. Maybe Jack!Rogers struck a deal with/strongarmed God into fixing him up.
 * There are loads of different ways he could've fixed his voice box after winning, from the extra Rapture medkits he had in his pockets to doctors back home.

The Big Daddies are Heavies in diver suits.
Like the Heavy, they're big, tough, simple-minded and carry really big guns. The Heavy is also a defense class, which explains why the Big Daddies are so protective of the Little Sisters. Speaking of which, the Big Daddies/Heavies most likely see the Sisters as Medics- like Medics, Little Sisters have fast healing powers that everyone wants and carry big needles.

Ryan Industries got help from Vault-Tec when constructing Rapture.
Rapture is an underwater city that was built on the idea of protecting private industry from 'parasites' and to test objectivist ideals and was supposed to be able to function for a long time. Vault-Tec vaults are underground vaults built to protect it inhabitants from nuclear war,, and to function for up to 200 years without outside support. Its quite possible that Vault-Tec helped build Rapture as a prototype underwater "Vault" that would let its inhabitants survive a nuclear war while having access to fresh fish and water (since any radioactive fallout would be diluted by the entire ocean before it reached the occupants) and used their technology to build the various life-support systems and extra durable alloys. Vault-Tec probably offered much of their work for free  which greatly appealed to Ryans love of cost-cutting.

The "First Big Daddy" is
Tenembaum just After all,
 * Jossed. The plot of Bioshock 2 clearly shows that this theory wouldn't fit.

Jack isn't actually Ryan's son, or the child that Fontaine and Suchong grew and programmed... he's just an escaped mental patient who does what people tell him to.
While 'Jack' did obey Fontaine's and Ryan's orders when he was given the 'Would you kindly' phrase, he also obeys Dr. Langford to get the rose, Sander Cohen to kill some people to get their pictures, Peach Wilkins to risk his life to get a camera and take photos of Spider Splicers, and Tenenbaum to have himself turned into a Big Daddy simply to get through one door when he could have tried using dynamite instead... all without one of them using the code phrase. Its quite possible that the 'real' Jack tried hijacking the plane only to have a mentally retarded mass murderer eat him and wear his clothes. Then 'Crazy Jack' went into Rapture and pretty much filled the same role as the 'real' Jack would have, that's why Fontaine failed was because his supposed puppet wasn't really a puppet... just some crazy guy who kills people as soon as look at him unless they ask him to fetch stuff. 'Crazy Jack' is probably a drug addict since he has no qualms with sticking random needles into his arms. The reason the Bathyspheres let him move around is because the so called 'sensors' that excluded anyone except Ryan from using them were made by the lowest bidder and just let anyone move around... Atlas could move around to help you and Sander Cohen could mess with them as well. The heart troubles from the Code Yellow phrase was just the natural result of all that splicing and eating cheap food off of burned corpses catching up with him (Tenenbaum's attempt to remove programming from his brain that was never there in the first place might have been a factor as well). And Ryan wasn't actually controlling Crazy Jack during the cutscene... Crazy Jack was just playing around until Ryan asked him to beat his head in.
 * But then how would he be able to use the Vita Chambers?
 * He doesn't. He's just imagining them because he's utterly insane. That's why nobody mentions or uses them.

The true best ending is the player turning the game off after Fontaine orders Jack to prevent Rapture from self-destructing.
It's fairly obvious that Jack's susceptibility to Fontaine's mind control is an in-universe representation of the player's desire to follow Fontaine's orders in order to progress in the game. It's been noted that the last third of the game, when the player is supposedly "free" from Fontaine, is noticeably lower in quality and really only involves the player switching allegiances to Tenenbaum. This is because, while Jack may be free from the code phrase, the player is still accepting the requirements provided for him to progress. The only way to free himself from Fontaine is to voluntarily give up the desire to progress by switching off the game, and letting Rapture be destroyed.
 * Alternately, he bucks Fontaine's control and shuts off the game just before killing Ryan; when he reaches the room just before Ryan with the recordings and such that cause him to realize how Atlas has been controlling him, he stops right there and does not proceed to Ryan's office. Perhaps, realizing it's just triggered by words, he turns off the radio and then politely asks himself not to kill Ryan, wiping his orders and preventing Atlas from sending him any more.

The Big Bad of #2 will be a Russian Communist exiled for his refusal to give up his religious beliefs
It's been confirmed by Word of God that the Man Behind The Big Sister is a philosophical opposite to Ryan, so quickly-ask yourself what is the diametrically opposed belief system to the atheistic capitalism of Objectivism? Your Fridge Logic (and the fact that I gave you the answer) should allow you to puzzle it out.

As for his motives, he probably has an accurate view of the problems that led to Rapture's descent (unchecked greed, hubris, and Utopia Justifies the Means), so he wants the Big Sister to help him create a Marxist paradise where Splicers live in relative harmony...Ironically falling into the same trap Ryan did, and resorting to hypocritical actions to force Splicers in line.

If this is true, then he's probably the founder of the "Cult of Jack" we've seen in the interviews.
 * Wouldn't Fontaine count as an ideological opposite of Ryan as well, In a Neutral Evil sense? Ryans speech in B1 could peg his ideological opposite as anyone from the CIA to the Vatican. Then again, I did hear what sounded like Russian on the Something in the Sea radio, so this could have some truth to it.
 * Jossed.
 * Ah-ah-aahh! It's actually confirmed, sort of.
 * Agreed. This theory has

Tenenbaum did not realize who Jack was until the last minute
Tenenbaum and Suchong built Jack's mind control, so if I had to write down a list of three people in the entire world who would know who Jack was and what the command phrase was, one of them would be dead at the start of the game. It seems odd that, as determined as she was to get him to help the little sisters, she wouldn't force him to do so--unless, of course, she didn't realize that the person she was speaking to was the boy whose mind control she had set up. Presumably, she doesn't figure this out right up until he breaks into Ryans office, at which point she realizes that the only explanation for his deeds to this point is him having Ryan's DNA. Or perhaps she doesn't realize it until the little sister rescues him from the office and she has a chance to examine him up close. After that point, ordering him to rescue them wouldn't do any good because she cures him of the conditioning before the next time he'd run into one (and she has to do that or Fontaine can keep using him). I suppose this makes her more than a bit slow in the head, but she's a science person, not a people person.

Atlas and Tenenbaum let Jack choose what to do with the sisters to prove a point
The only alternative to the above. BOTH Tenenbaum and Atlas know that all they have to do is say the magic words and Jack will do as they say. Both strongly urge him to take a certain action against the first and all subsequent little sisters, but even as they see you moving to obey the other, neither will order you to stop. Why? Tenenbaum thought of Jack as a son, just as much as she considered the sisters daughters, and really, really wanted to believe that, at least to the extent that he had any free will, he could be a good person. So she wanted him to make the decision to help the sisters on his own. Atlas, meanwhile, wanted to rub in Tenenbaum's face how her moral high ground wasn't shared by the rest of the world and, most especially, her "son", so he wanted Jack to choose the path of selfish expediency on his own. Although the sisters' lives were in the balance, neither would be well served by ordering Jack to do what they wanted, and both knew it. The contest was set up by almost spontaneous unspoken agreement the minute the choice came up. Besides, both knew that if they tried to give an order the other could try to go over their head, and it would devolve into a shouting match which would almost surely reveal the truth to Jack (which Atlas, at least, didn't want). I suppose if not for that last detail Atlas would have been almost as well served by ordering Jack to defy Tenenbaum, but he had more to lose from exposing the secret than she did.
 * Considering that Tenenbaum PROBABLY had no idea who Jack was on their initial encounter, having had no knowledge of Fontaine's use of Jack as a time bomb, she probably realized it too late to have an affect.

Jack is hallucinating both endings
He really got killed when Fontaine became more plasmid then man. Jack was actually lying on the ground,imaging that he was saving the little sisters or taking over the world,while he slowly died. He never escaped and never beat Fontaine.I mean,Fontaine is basically Superhuman in every way,no man could beat him on the first try,even with the amount of guns Jack was carrying,but Jack probably got the last laugh when Fontaine got killed by the little sisters in a revenge attack. Sadly,though,they were a little too late.
 * This actually could explain why nobody seems to know exactly what happened to him after Fontaine's death. If he dies after that titanic battle, he won't lead splicers in an attack on a nuclear sub nor will he lead the little sisters to freedom. Which, now that I think about it, explains where Tenenbaum is during that sequence. He's imagining what Tenenbaum would say to him, given his previous actions in-game.
 * There are a fair amount of Big Sisters in Bioshock 2, and they're basically, so it's quite possible none of them were saved. However, Subject Delta never goes back to any of the areas that Jack visited, so unless we find out what happened to those places, we can't really know that fate of the Little Sisters. It's possible all the Little Sisters that Jack saved were just saved by Tenenbaum, if Jack died.
 * If Jack was unable to defeat Fontaine because he was superhuman, then you'd better guess again, 'cause Jack is too. The only real difference between Fontaine and Jack was Fontaine was stronger, but was unable to use weapons. And Jack can use a Vita-Chamber, so how exactly would he die if he could just come back and wither down Fontaine's health? Plus, Jack had a grenade launcher, a Tommy-Gun, a revolver most probably designed for killing bears, a device capable of LITERALLY THROWING ELECTRICITY, a crossbow, a very large-caliber shotgun, and a wrench, as well as the ability to fling every single element of nature from his hands at will. Yeah, Fontaine's going down like a corpse with cement-block shoes.

The turrets, security bots, and cameras are run with genetically-engineered brains, not just "steam forming allegiances"
Think about it. If it were purely mechanical, you wouldn't be able to hack them, especially with the green liquid that the first game used. The hacking method is to blank its mind out, so that it sees Jack and anyone with him as friendly, and anyone else as an enemy.
 * In a sense this WAS the original plan. Early concept art and dev interviews all but confirm that the minigame was originally created with the plan of it being a drug that made the organic elements of the shops, turrets and such happier, something that was given once the right amount of money was given. Hacking it would lower the demands of the little mutant inside. Ultimately it was abandoned with a LOT of early design stuff, most of it because it was VERY similar to System Shock (Originally it was going to be the sea slugs that caused the downfall of Rapture, much like The Many in System Shock.

Jack isn't "hacking" the cameras and bots, but fixing them.
Like the VitaChambers, the cameras and bots are designed to recognise Ryan's DNA. When things went out of control, Ryan set them all to "kill everyone but me", to keep the splicers from roaming freely throughout Rapture. But they managed to reverse them to "kill nobody but me", which is why they attack Jack and nobody else. Jack is simply restoring them to their intended settings.

Big Daddy is an ancestor of Iron Man
They look so similar to Iron Monger in the movie that it probably just isn't coincidence. One of Tony Stark's ancesstors (most likely his grandfather) worked for Ryan and helped develop the Big Daddy. However, he soon sneaked out after seeing that Rapture was going to pieces. This would explain how Tony built his first suit because he knows from his grandfather how to build a Big Daddy (which is essentially a mech-suit) with parts 50 years old.

Sander Cohen is the Phantom
Perhaps the Phantom would emerge years later, and in secret, as Cohen. What they both share in common.
 * Both are deformed and could be seen wearing a mask
 * Both are mad artists.
 * Both effectively run the theaters they occupy

Differences I acknowledge:
 * Different backstories. If Cohen was indeed the Phantom, then the past we know of from him, as well as his audio diary portrait, will be a fabrication.
 * Cohen's sexual orientation is ambiguous, and he was not known to have had a romantic relation with, let alone try to seduce, a person of the opposite sex.
 * The phantom murders only those who try to get in his way. Cohen seems to murder or torture for the hell of it, though he especially gets mad when his work gets disrupted or if you just piss him off like Fitzpatrick, Rodriguez, Finnegan and Cobb apparently did.

The Third Bioshock Villain will be a Corrupt Church Knight Templar duo
Remember when Andrew spoke of how if a man's sweat is entitled to his brow. He mentions the church along with the US (His former ideals) and the Russians (Sophia's ideals), so the church's representative would be two brothers who shall follow the same fates as Cain and Abel.
 * Not quite sure. Sophia Lamb also had a great number of religious ideals and extremism in addition to her collectivist beliefs.
 * For the religious duo, they believe only God deserves the sweat on the brow, theirs included. The difference how one gets sweat off the brow. The Abel version believes only their sweat belong to god and that the society should be relatively closed off to outsiders but is a heavy supporter of ADAM (which he believes is God's blood). Cain on the other hand wants to use outsiders as slave labor to get the sweat. Its more complicated then it's sounds and the message isn't exactly God Is Evil.

The Third Bioshock Villain will be a Nihilist
He believes in nothing and manipulating people is his only joy in life.

Random Bioshock 2 Plot Guesses
Just a few predictions for the upcoming sequel:
 * As Subject Delta (The fourth Big Daddy, first one to successfully bond with a little sister) you will encounter Mark Meltzer (The guy from the There's Something Under the Sea website) and can choose to help him in his quest for his daughter
 * Eleanor Lamb (the little sister that Delta used to protect) will be a Big Sister who will have a Heel Face Turn and
 * The manner of death (at least in the good+ ending) is definitely Jossed:   If I ever were to cross paths with Eleanor, I would try not to piss her off. Wait, I just noticed it after re-watching. She gave Sofia a breathing apparatus in the good+ ending, so I'm wrong. probably lets her drown in the bad ending though. Must beat game and view all possible endings.
 * Depending on the moral choices you made during the game, you will either
 * Augustus Sinclair will be a Red Herring Atlas:
 * There will be a brief prequel tutorial in which
 * Sadly Jossed by the emergence of the first five minutes:
 * Either you will be related to or Sinclair gets you access to the Vita Chambers.
 * Confirmed, because of respawn footage.
 * In the multiplayer story the spawn points will be because Sinclair also developed the widespread ones.
 * Also in multiplayer, Danny Wilkins is related to Peach Wilkins.
 * According the the Bioshock Wiki, Jossed.
 * Regardless of ending you chose in the first game,
 * Orrin Oscar Lutwidge (another character from the There's Something Under the Sea website) will
 * Unlikely, as
 * Jeremiah Lynch (an antagonist from the There's Something Under the Sea website) will arrive in Rapture and you will have to stop whatever he's been planning.
 * Huh? Both the wiki and the Something in the Sea website fail to mention . Despite neither of them being in Bioshock 2, In what source is it said ?
 * It was at the final location party in L.A. we arrived hoping to meet Oscar or catch lynch and found two chalk outlines and some 'cops' who explained what happened. Then we went inside for a release party.
 * Instead of being The Dragon to Big Bad  it actually turns out to be the other way around
 * At some point some of the former minions of either Ryan or Fontaine will This choice will mirror the choice of keeping Sander Cohen alive in the first game. Your choice will either get you immediate reward or you will be rewarded by the employer with advice for taking down  or
 * As for the plot twist,
 * Orrin Oscar Lutwidge (another character from the There's Something Under the Sea website) will
 * Unlikely, as
 * Jeremiah Lynch (an antagonist from the There's Something Under the Sea website) will arrive in Rapture and you will have to stop whatever he's been planning.
 * Huh? Both the wiki and the Something in the Sea website fail to mention . Despite neither of them being in Bioshock 2, In what source is it said ?
 * It was at the final location party in L.A. we arrived hoping to meet Oscar or catch lynch and found two chalk outlines and some 'cops' who explained what happened. Then we went inside for a release party.
 * Instead of being The Dragon to Big Bad  it actually turns out to be the other way around
 * At some point some of the former minions of either Ryan or Fontaine will This choice will mirror the choice of keeping Sander Cohen alive in the first game. Your choice will either get you immediate reward or you will be rewarded by the employer with advice for taking down  or
 * As for the plot twist,
 * At some point some of the former minions of either Ryan or Fontaine will This choice will mirror the choice of keeping Sander Cohen alive in the first game. Your choice will either get you immediate reward or you will be rewarded by the employer with advice for taking down  or
 * As for the plot twist,
 * As for the plot twist,

The sea slugs that create ADAM are close relatives of Elysia chlorotica
Elysia chlorotica is a species of sea slug that steals chloroplasts from algae to make its own food. It can also pass the genetic material for chloroplasts down to its children, though they have to eat more algae to do the same as their parents. The ADAM slugs are part of this family, except they merely have a rather unstable genetic code, which was how Dr. Tenenbaum was able to make plasmids out of their genetic material.

ADAM is The Virus.
There's still plenty of ADAM available after seven years of a dependant, mostly deranged population has lost the ability to easily manufacture more? And mutations have apparently been getting steadily worse? Perhaps ADAM, if not regularly exposed to more, begins to take over the body.
 * Lamb was making more Little Sisters by kidnapping children from coastal cities; by the time Subject Delta wakes up, there are enough to go around.

ADAM comes from Adam.
Like LCL came from Lilith. The evil-ending Eleanor (or possibly even the good-ending version) may also have ended up creating/joining SEELE. Feel free to come up with other implications.

The Vita-Chambers are able to self-repair themselves.
The reason that the Vita-Chambers are still active and working after so long without anyone doing maintenance on them is because their resurrection field affects themselves and automatically fixes any damage or wear and tear they endure. This was built into it by the designers so that they don't have to pay anyone to fix them and better helps them keep the Vita-Chamber technology a secret (since its self-repairing then they don't have to tell anyone how to fix them and therefor it would be an uphill battle trying to figure out how they work). As a side effect, people like Ryan or Lamb can't order their minions to smash the Vita-Chambers and rob the protagonist of their ability to resurrect and anyone trying to program their own DNA into the system would have a hard time figuring out how to do so.

The Big Daddies are Tragic Monsters
because their entire purpose in life is one giant Escort Mission. Imagine playing the "protect the Little Sister" missions in Bioshock 1 and 2, for the rest of your life.

Sander Cohen survived the events of the first Bioshock
After completing his Quadtych, it is ultimately up to the player if they wish to kill him or not and the reason why we didn't see him in Bioshock 2 is because Subject Delta didn't go anywhere near Fort Frolic thus never meeting up with the still alive Cohen.
 * On the other hand, Sofia may have killed him and used his Adam in her Assimilation Plot. In fact, that might explain why Alex the Great wound up so horribly wrong.

Sander Cohen was killed by Jack, but was revived by a Vita-Chamber
During the events of Bioshock 1, the Vita-Chambers would only revive someone with Andrew Ryan's genetic code. However, consider the following three factors:

1. Sander Cohen is a powerful Houdini Splicer, whose ability to teleport and throw fireballs allow him to travel quickly and safely throughout the city. 2. While Cohen is clearly insane, he appears to be relatively well grounded (for a splicer, of course). So while he occasionally freaks out and kill people if he feels they don't appreciate his work, he often retains his composure and is alert and lucid, unlike like most citizens of Rapture, completely lost in their own little worlds, aimlessly wandering the corridors muttering their respective Madness Mantras to themselves. 3. There are hints in the game which suggest Cohen and Ryan were romantically/sexually involved.

Taking these points into account, It's possible that even after the city fell into chaos and Ryan locked himself in his office, Sander could still periodically teleport into Ryan's office if he felt like it, and as long as Ryan didn't say anything unflattering about Sander's new "Plaster Period" Cohen would have no reason to kill Ryan.

Therefore, it is possible Sander was able to use the Vita-Chambers if he was in the possession of Ryan's "genetic material".

Ryan and Lamb each represent a type of online gamer.
Ryan's objectivist ideals entail that you sacrifice all charity, kindness, etc. for the sake of progress and personal gain. This is not unlike your average spawn-camping, kill-stealing, glitching/cheating jackass who does whatever it takes to win and rank higher on the leaderboards.

Lamb's ideals sacrifice individuality, free choice, etc. for the sake of unity. In essence, she is a Stop Having Fun Guy trying to enforce "Fox only! No items! Final Destination!" for the sake of Competitive Balance.

Eleanor Lamb will be the central character of Bioshock 3.
2K will also pull a Mass Effect and have you transfer over your game-completion data from Bioshock 2, thus influencing who Eleanor is and what she does in Bioshock 3. After all, you've just spent the entirety of Bioshock 2 helping define Eleanor's morals, it would only make sense for something like that to have an impact on the next Bioshock.

Biochock 3 will involve plasmids being used on the surface.
Eleanor's comment in the good ending that it would be easy "to misjudge them", indicates that she believes she won't be accepted by the surface dwellers. This will indeed come to pass, as Eleanor will be captured by the military in order reverse-engineer Plasmids from her DNA and will be forced to divulge the location of Rapture, which will be enthusiastically plundered by the world's governments (possibly starting up a war between the US and USSR over who can get there first). The game will take place after Eleanor has started up La Résistance to stop a power-mad new regime from repeating the mistakes of Rapture.
 * Sorta confirmed...though not involving the plotlines here at all and takes place above the surface.

Bioshock 3 will be much more survival-horror-y than its predecessors.
Bioshock 3 will be set at some point in the early-to-mid seventies, with Rapture's food/water/ammo stocks near zero and the overwhelming bulk of its population too far gone to make more. Most of the Splicers will have become cannibalistic and some of them will be mutated to the point of being barely recognizable as human. Additionally, Rapture continues to decay and large parts of it will be increasingly submerged as the Big Daddies cannibalize the architecture for parts to fix the salvageable areas.
 * Jossed.

Taking all bets for Bioshock 3's protagonist.

 * Eleanor!
 * A member of the CIA/KGB/Military/a mercenary group who happens to find Rapture.
 * Tenenbaum, on a quest to stop Evil Jack from detonating the nuke and starting a war with the surface (Nobody said it had to continue on from Bioshock 2).
 * I like that theory. Bioshock 2 is a continuation of the good ending, Bioshock 3 continues the "you're a heartless dick" ending.
 * Cindy Meltzer, assisted by Tenenbaum, out to take out Evil Eleanor. Big Sister on Big Sister action!

The ADAM-producing slugs don't live in the stomach; they're actually in the
This Troper admits the following theory is messed up and sacrilegious and also probably Nausea Fuel, so I'll put most of it in spoiler tags. And now I'll go make myself taller for ruining this fandom with my horrible mind. Apologies!
 * This Troper had a much less squicky version of this WMG. Instead of, the slug just  . Also while we're on the subject of the reproductive system (And since the WMG tags don't seem to be working for me)   didn't splice away his balls. He has the Armored Shell tonic equipped and a side effect/feature of the tonic is to cover genitalia with a natural cup made of whatever Armored Shell is made of.
 * Just posted in It Just Bugs Me where someone else had a similar idea. Short story: nah. One of Tenenbaum's diaries explains that the Little Sister needs to regurgitate the ADAM-laced blood/goo/whatever in order to mass produce it. Judging by us not seeing Big Daddies molesting their Little Sisters in order to get the ADAM out of them, we can safely assume that that's one place the slugs most certainly aren't.

Eleanor is Frank Fontaine's daughter.
Check out the wall painting in Fontaine's office. Doesn't the kid look familiar? Admittedly, the exact gender of the kid is up in the air, because the painting isn't very distinct, so it actually could be young Frank, but this is Wild Mass Guessing, dammit.

Tenenbaum has been using extremely powerful prototype plasmids for a while now to keep herself alive in Rapture, and she's still sane because she implanted herself with an experimental ADAM slug.
It may be far-fetched, but let's consider the evidence- one, surviving in Rapture for the events of both Bioshock 1 and Bioshock 2 takes a lot out of a person and this troper thinks it highly unlikely that most people could make it without plasmid assistance.

Two, Frank Fontaine himself highlights this by saying, "If you survive World War II and Rapture without so much as a scratch, you got more than leprechauns watching over you."

Three, Tenenbaum was one of the few people there in Rapture practically since the beginning. Since she had the authority to start up the Little Sister program and all that, it's not unlikely she was able to develop certain abilities in the field of plasmids, for survival's sake. A person with her authority should have no trouble getting her hands on, say, a plasmid that makes your body indestructible or a plasmid that psychically repels Splicers.

The bit about the ADAM slug is also possible because Tenenbaum practically made the Little Sisters herself, and if anyone would know how to implant those slugs into someone who's not a Little Sister, it's her. As for why, it's revealed in the sequel that people with Little Sister ADAM slugs and the like, such as are immune to the effects of Splicing, and by dabbling in some forbidden science, which is within her ken, naturally, Tenenbaum is able to remain immune to the effects of plasmid use while being able to stay alive in a nightmarish place like Rapture.

Subject Delta is Eleanor's literal father.
We are never told who Eleanor's father was, only that Sophia seemed to have no time for romance after arriving at Rapture. Subject Delta, in his persona as Johnny Topside, came to Rapture for as yet undisclosed reasons. Word of God said that Subject Delta's past was supposed to heavily parallel with Mark Metzer's. Eleanor also seems to regard subject Delta as her true father. With this in mind - we can connect the dots. Delta is Sophia's estranged husband. After the Lambs vanished to Rapture, he, like Metzer, searched the world for his daughter, eventually discovering Rapture and becoming a key player in the civil war. He, like Metzer, was also turned into his own daughter's Big Daddy.
 * Halfway Jossed. There's an Eleanor-Vision that was removed from the final game showing this, but the developers didn't want Subject Delta's backstory to get too developed.

The Third Bioshock game will be about Tenebaum
Or more specifically her own adventures a little before, during, and a little after bioshock 2, detailing how she got out of Rapture with her flock of little Sisters. Possibly going somewhat by the WMG two up (the one about her using prototype plasmids), she could be a midway between Jack and Delta in terms of power and strength. Though such a game would regretfully be far more linear in morality choices, or reflected more on interactions with other NPCs more than the Little Sisters.
 * Jossed.

Security Chief Sullivan killed Suchong
Sullivan was one of the few people in Ryan's adminstration who seemed to notice how screwed up things were, and Bioshock 2's loading quotes reveal he was the one who discovered Suchong's body. Feeling guilty over his own actions, and wanting to prevent more damage from being done by the mad scientist, he murdered Suchong and faked an audio tape to implicate a Big Daddy. Furthermore, when we discover Suchong's body the drill seems stuck there, which would seem improbable if the hulking Big Daddy did it.
 * Judging by Delta and Sigma, the Alpha series Big Daddies have hand-held drills they can swap out for other weapons, which could have been left in Suchong.

Letting out Gil is not a good idea
After fulfilling his promise to "Live Outside", his body continues to mutate, making his a gigantic monster that wanders the Atlantic, eventually settling down for hibernation as his body continues to twist and his mind slowly degenerates. A long time later he is awoken by a satellite to the head, confused, he ends up coming ashore in New York and wreaks havoc on the city and its populous, including a few douches with a camcorder.
 * But what about the Parasites, you ask? Insect Swarm, level 10 or so.

The endings in Bioshock 1 branch off into different storylines.
For the good ending, Jack and his Little Sister pals live long lives and Bioshock 2 happens. But with the bad ending, Jack launches the sub's nuclear missiles, that hit both China and the USA, making them think that the war between them had begun. With this war, both nations fire their entire nuclear stockpile, bathing the world in nuclear fire. A few Splicers remain, and they become Feral Ghouls, mainly Glowing Ones and Reavers.
 * China didn't gain nuclear weapons technology until 1964, four years after the game and the bad ending take place.
 * More damning, in Fallout the bombs fly on October 23rd 2077.
 * Soviet maybe?

Jack has an ADAM slug.
Little girls are the only subjects that can be implanted with slugs to successfully yield up to thirty times the amount of ADAM and gain super healing. It's never stated why other hosts wouldn't be "viable". Perhaps they merely didn't multiply the ADAM output. Jack was implanted with a slug that produces ADAM at an almost worthless rate. The ADAM built up in his body during his entire year on the surface was all blown on Electroshock. However, caffeine and nicotine can cause it to generate Eve. More importantly, even though his cells couldn't regenerate like the Little Sisters, they gained the immunity to the symptoms of splicing that the Sisters have, leaving him free to splice at his leisure without fear of insanity or mutation. This was Fontaine's insurance policy against Jack's plasmid-induced super aging driving him insane while on the surface. If you like, this slug also slowly grew back his vocal chords after the Big Daddy conversion, thus undoing the major continuity error of every postgame fanfic ever.

Rapture is developing a sustainable food chain consisting entirely of ADAM.
Little Sisters take in the old ADAM, serving as scavengers and decomposers. It's entirely possible that they can subsist entirely on this. Their waste product (recycled ADAM) is distributed among Big Daddies (just because only the Alpha series gets properly weaponized plasmids doesn't mean they're not all heavily altered) and possibly used by whoever's in charge (Ryan or Lamb or whoever) to bribe splicers. Splicers and occasionally Big Daddies and Little Sisters become food for larger, tougher splicers. Big Sisters are the top predators. Incidentally, they make a lot of sense viewed from this perspective. The "increased aggressiveness" of older Little Sisters was just them getting hungrier, as pubescent kids do, and beginning to see the splicers as Happy Meals with legs. They don't care about keeping ADAM in the food chain (like lions don't care about making food for dung beetles) or protecting the Little Sisters (at the very least, it's not a primary objective). They attacked Delta because he was a delicious four-course meal. Then the Big Sisters throw up ADAM for whoever's holding their leashes, the ADAM is given to splicers who start killing each other over it, and the cycle begins anew. For all we know, none of them even need food. Delta's gluttony aside, it's hard to see how Big Daddies would eat. The only necessary inputs are more people because I refuse to accept the possibility that splicers aren't sterile.

People who are naturally psychic aren't affected by the psychological side effects of splicing.
Suresh Sheti (from Bioshock 2 multiplayer) seems to be one of the few sane splicers. Furthermore, his diaries imply that he had telepathy long before splicing. Perhaps because he is already used to mental abilities, the splicing didn't affect his mind.
 * Or, it could be that Suresh Sheti wads functionally insane and just hearing voices in his head and thus he was crazy to begin with, Crazy Awesome that is.

Using Vita-Chambers have some additional effects.
Such as reducing the effects of alcohol and increasing metabolism speed tenfold! How else could Jack/Delta down whole bottles of moonshine and only get drunk for about 20 seconds with no hangover afterward, and devour potted meat by the refrigerator-full and not feel bloated or sluggish?

Delta has a built-in can opener.
Think about it. Jack couldn't eat canned food.
 * Now that you mention it, part of the drill looks an awful lot like an automatic can opener.

Delta was still under Big Daddy conditioning/mind control, but his orders were always vague and few, allowing him to emulate free will
With Eleanore unknowingly being the one in control, in the end, Eleanore never told Delta to kill or spare anyone, and thus the objective she gave him (rescuing her) was one of only a handful of solid orders she gave, and on those occasions, he was basically free to come to his own conclusions as to whether to kill a potential future threat to his little sister, or not waste the time, this "Save Eleanore" logic could extend to the choice of saving or harvesting the little sisters, saving them to make her happy (or your conditioning for Eleanore extends to them too, unknowingly), or harvesting them to increase your odds of saving her. The conditioning wasn't truly broken until Sophia broke their pair bond. But most of all, the irony it brings to the table on Sophia's arguments about Delta being a monster of the Self as well as the common ground it gives him with Jack is why I like to imagine this.

Eleanor Improved Delta when she brought him back to life.
This is based in part off the in-game Alpha Series, as well as the opening cutscene. We only ever see Delta using the drill officially and we only see Alpha Series using Machine Guns, Launchers, and Shotguns. In other words, the things you don't need to aim precisely. This implies that the Alpha Series suffered from inaccuracy, be it from poor vision or poor thinking capacity, thereby rendering them unable to use precise weaponry. Also, when Alpha Series "use" their plasmids, they merely shoot out an impercise field of ice, fire, or electricity. Delta, however, can use all the properly-sized weapons he finds, even the Spear Gun, and can aim his plasmids at what he wants to hit. If we assume Delta was no different from any other Alpha Series, then the jump to believing Eleanor improved his genetic code isn't that hard to make
 * Orrrr it could be that (as was explained in-game) the Alpha Series went insane when the pairbond experiments on them failed. Delta was the first success.

ADAM was tested on Adam.
The Healing Factor provided by the ADAM slug in his stomach is why he is able to stay along Jamie for so long without turning into chunky salsa. This fact, combined with the Little Sister mental conditioning and exposure to Impressive Pyrotechnics led to an unusually deep fascination with rapid pressurized disassembly of large objects.

If there is a Bioshock 3, the player character will be Billy.
Having somehow survived the flooding of Dionysus Park, Billy will grow up to be a jaded splicer, who does a Heel Face Turn after seeing his childhood crush alive and well... but as a big sister.

The telekinesis plasmid works by sonic manipulation.
Ever wonder why there is always a distorted humming sound when in use? It's not there to help you, it's how your powers work. Try using a telekinesis on a object that's behind a shop window and you will find it won't move, the simplest reason is because the medium of air need for your powers is blocked by the glass. The Dummied Out Sonic boom plasmid makes the connection with sound even clearer, it behaves exactly the same as a telekinetic throw and even has the same audio and visual effects.

The plot of Bioshock 3 will be as follows.
The Big Bad of Bioshock 3 will be Orrin Oscar Lutwidge, who was a character who was featured prominently in the "There's Something in the Sea" viral campaign that preceded Bioshock 2's release and by the end his final fate is left ambiguous. While he may have died his body isn't accounted for, and his background reveals he not only once went to Rapture but expressed a desire to return to it. Having already been noticably mutated by splicing in his original visit to the city, Lutwidge wouldn't immediately be considered an outsider (and thus, not marked for death) by it's inhabitants but because he hadn't had the opportunity to abuse ADAM as much as they had due to leaving he retains much of his mental abilities (if not sanity). Using his genius engineering talents, he is able to save the city from completely falling apart following the departure of both Ryan and Lamb, uses his charisma to get the remaining splicers to name him the new leader of Rapture, and as a huge fan of Lewis Caroll, he turns Rapture into a creepy "Alice in Wonderland"-themed environment. And rather then trying to make Rapture an ideal free-market or collectivist society like Ryan or Lamb respectively, Lutwidge (who was less sane then either of them) turns it into utopia for the insane, where splicers give free reign to their psychotic tendencies, making them more dangerous and upredictable then ever. "Chesire Cat: We're all mad here. I'm mad, you're mad.

Alice: How do you know I'm mad?

Chesire Cat: You must be, or you wouldn't have come here."

And then, as Rapture is basically on its last knees, the US Government and Soviet agents show up to crash the "tea party" just as Ryan always feared. Which is when Lutwidge's Xanatos Gambit is revealed,
 * This is the best Bioshock 3 idea ever
 * You win TV Tropes!

Johnny Topside, a.k.a. Subject Delta, was the inspiration for the creation of Big Daddies.
Johnny Topside was a diver who discovered Rapture by accident. Most people in Rapture were probably terrified that someone from the surface could ever find the place and get in, especially if Rapture had been around long enough for a generation of children to grow up with the scare tactics at Ryan Amusements drilled into their brain (even Ryan himself thought that ride was too much). Suchong noticed this when it became necessary to design a protector for the Little Sisters, so heused giant, angry diving suits to play on the citizens fear of the outside. Delta's suit may even be the very one he came to Rapture in.

Andrew Ryan was right!
At first. Rapture fell apart because he betrayed his own Objectivist principles and became mad with power, cutting off trade with the surface, not letting people leave, banning religion and placing belief in the "Great Chain" in its place (which Lamb pointed out in one of their debates, was essentially a faith in itself), and generally running the show like a despotic dictator. He could have found a way to preserve trade with the surface without giving away the location of his city, he could have let people practice their religion privately, or else leave if they felt their were being oppressed.

Ryan was splicing, and that is why he went crazy and betrayed his principles
First off, sorry if this has been said already. Ryan merely appeared healthy and normal because he could afford the highest-quality plasmids and tonics, and probably tested them thoroughly (on inmates of Persephone, most likely) to make sure they didn't cause immediate disfigurement or noticeable insanity. But the brain-and genetics-are both delicate, tricky things, and just because a plasmid didn't immediately make the user catatonic or frothing at the mouth crazy doesn't mean that it couldn't have subtler, long-term effects, such as making the user increasing paranoid.

Rapture is powered by the BP oil spill.
...Give me one good reason it isn't.
 * Rapture was built in the 40s, experienced a great amount of decay and destruction through the late 50s and 60s, and is located a ways east of Greenland.
 * Timey Wimey Ball. With portals.

Jack was in some way related to Raz

 * Given that both possess powers such as telekinesis (which they would pick up along the way), and.

Medkits are made from ADAM
When Tenenbaum first discovered ADAM, all that she knew of it was that it had healed a crippled man's hand. Logically the first thing she, and her financial backer Fontaine, would have done would be to use the ADAM to create a new medical wonderdrug, sell it to the public and put the profits into further research. This would also neatly explain how spider splicer organs function like medkits; The organs are ADAM rich and, thanks to whatever cocktail of tonics and plasmids make a spider splicer, ready to be turned into a rough equivalent of a standard medkit.

Delta is fed intravenously
Looking at his model, Delta has red and blue tubes on his back, presumably for supplying him with ADAM and EVE without him having to stop in the middle of a fight to recharge his ability to use plasmids. It's likely that he has a similar system for supplying his body with nutrition. Because Big Daddies are out in the field so much, it's also likely that this system allows for normal foods to be ingested. Thus when Delta eats and drinks the various food items you find throughout the game, he is not taking off his helmet to do so, but is instead shoving them into his suit's feeding system.

Andrew Ryan is Ayn Rand's Alternate Universe Spear Counterpart
Not only are their names very similar (not to mention similarly anglicized), but they have similar back-stories - i.e., immigrating from the Soviet Union, then becoming disenchanted with America. Rapture is Ryan's version of Rand's bibliography.

All the "Shock" games have elemental and extremist motifs - meaning that Levine's future projects can be predicted.
System Shock takes place in a space city where The Singularity causes a disaster, Bioshock takes place in an underwater city where Objectivism causes a disaster, Bio Shock Infinite takes place in a flying city where ultranationalism causes a disaster. Ken Levine's next project will be either a crossover with Fallout taking place in a giant underground vault or a some kind of geothermal city planted in a volcano where where either a Government Conspiracy causes a disaster, or an Animal Wrongs Group causes a disaster. His general theme seems to be "extremism is bad", so everybody will eventually get a turn. But given how much venom he put into his anti-transhumanism and anti-capitalism tracts, the ultranats better get hit hard.

Medic is Tenenbaum's brother
The vaguely cartoony art style, the 1960's setting, the level of technology, it all points to the simple truth that Team Fortress 2 and Bioshock share a universe. Two German siblings pursue careers in the field of medicine, forming a friendly rivalry with one another in their youth. But as the years pass, they drift away from each other, and head down darker paths. One to the city of Rapture, the other to the sinister world of mercenaries. Which leads to...

Bioshock 3 will involve the complete destruction of Rapture at the hands of a band of mercenaries
After two adventures in this city, Tenenbaum will decide that it must be eliminated completely, and call her brother and his team to do the job. Valve and Irrational Games will come together in one glorious moment of 1960's-style violence and destruction to give the fans of both the one thing they really want; a chance for Heavy to wrestle with Brute Splicers and Big Daddies.

Jack is Gman.
In the Half Good/Half Bad ending, Jack becomes a splicer. What if he, instead, went on the ship that those men were on when the splicers killed them, and then went back to land? Along the way, he discovers a way to become a Time Lord and from there controlled many peoples lives (For teh lulz, I assume), including a certain...
 * But you could say that with anyone, couldn't you? "Master Chief goes to Halo, finds way to become Time Lord, becomes Gman."

All of the sequels to Bioshock will systematically deconstruct various ideologies (at least in their extreme form)
My guess is Anarchism will be the one to get the next treatment, what with it being practically the near diametric opposite to the ideals of Columbia. One might also speculate that different forms of Communism/Socialism will get a treatment as well. Ones that stand out as being ripe for the picking, if you will, include Trotskyism and Maoism/Anti-Revisionism (both of which are essentially diametric opposites to each other within the confines of Marxism-Leninism). Others could be Agrarianism and Fascism (though the latter has been done to death already....).

Eleanor Lamb is Jack Ryan's half-sister
We don't know who her father is, but she does have dark eyes and hair, mist likely taken from her father. There are many dark-haired and dark-eyed men in Rapture, but if Sophia's daughter was Ryan's daughter, it would be good political leverage, and Sophia could make Eleanor the rest ruler of Rapture. She most likely didn't know about Jack, so she thought Eleanor would be the only child.

After the Rapture and Colombia timelines, the final Bioshock will take place IN SPACE!
Because once you've done stories about failed utopias in the sea and the air, space is the logical last place you can set a game.

Brenda is related to Andrew Ryan
This troper noticed that, in the fight area before you go to the Medical Ward, sometimes when the splicers come through the wall upstairs, a female splicer will say "You killed my Charlie!". The splicers in the Kashmir Restaurant are Charlie and Brenda, and this can occur even if you killed Charlie and Brenda. The logical conclusion: That Brenda is somehow related to Andrew Ryan, and can use the vita chambers.

ADAM has turned all splicers into clones of strong personality types
That's why the all look and sound alike, the original of each was killed and their ADAM harvested, when it was injected into another person it began transforming them into copies of the original.

The "Best" Good Ending of Bioshock 2 is actually horribly ackward.
When Elanor absorbs Delta so that her "Father" would always be with her, she may not have considered what it would mean when she has to go to the bathroom or more intimate activities.