Dead Space 2/WMG

The Markers are an invitation to a party filled with Higher Beings
The Markers were created by an ancient intelligence as an invitation/escape for intelligent species that are too advanced to sustain their growth without resorting to unsustainable practices like planet cracking. No alien life has been discovered in Dead Space because they all accepted the "invitation", Earth's being the Black Marker. "Convergence" is the process by which ALL the "potential" of an individual is combined with all other individuals into some sort of Cosmic Being. This process doesn't require the individuals to be alive however, so the Marker just rounds people up in the most efficient way possible, making us do it for it. Sort of like how in Evangelion everyone gets turned into bio-juice stuff that melds consciousnesses into one intelligent ocean that was supposed to be a "perfect" existence. So basically humanity is clinging to life in its current form out of fear of Glorious Convergence! Also, the Hivemind was just an efficient pre-convergence "standby phase" for the necromorphs to take as the Marker waited for its builder to return so it could trigger a Convergence. The Marker wanted to be returned to the Pedestal so that it could hide the necromorphs again as it waited for its builder.
 * This is interesting, but I don't like the direction it's headed, what with the seeming implication that the "Invited" aliens are just misunderstood. Either way, they still result in the deaths of a lot of people, including BABIES AND CHILDREN, and also make us look freakish and go batshit-insane. I think that's reason enough to go on killing them.

The Markers are capable of free choice
The Markers are clearly intelligent, and capable of controlling organic life through hallucinations. However there is some disparity between the actions of the markers in the first game and this game. My theory? The markers are sentient but the Titan station marker chose to be evil, while the Aegis 7 marker chose to be good, possibly from the centuries of quiet introspection and isolation. Necromorph creation is probably involuntary, which is why the Aegis 7 marker wanted to be returned to it's pedestal, so it couldn't hurt anyone else. the Titan Marker, being younger chose to be evil because it likely suffered from increased ego from being 900 feet tall, and thought it should take over the universe.
 * I doubt that Markers have things like Ego, just desire. I also doubt that age factors into the equation, here. It's possible that, assuming the Markers can be affected by the environment they were created in, the Yellow Marker (the Site 12 one) was simply made to be an absolute sociopath by the cruel Earth Government, and learned early on that the only way to avoid being used for the rest of time as an energy source was to manipulate the scientists into giving it control.

Convergence creates a new Hive Mind
Considering our dear friend the regenerating Implacable Man looks an awful lot like a more humanoid Hive Mind (with those five eyes and all) and that the Marker needed lots of bodies, it's possible.
 * However, the Implacable Man makes an appearance when you first let the Necromorphs swarm the government sector. If you look, you'll see him. How else would an army of Necromorphs be able to swarm over 200 heavily armed men so quickly? One of them is literally unkillable! However, this is still likely. However, it is possible that the Hive Mind in Dead Space was malformed or a mutant, due to the fact that the Red Marker was a failed experiment.
 * It is possible that Convergence is what creates the hive mind, and then the Marker goes dormant to control it. It would explain why the Site 12 Marker behaves differently than the black or red markers: the older ones have achieved convergence and are now content on being dormant, while the "young" one has yet to converge.

The Nicole hallucinations are actually trying to help.
Yes, we all know that mostly when she shows up our pants get filled, but she's giving rather pointed reason why you suck speeches. Then comes the hallucination in the mines where Isaac finally admits how important Nicole was to him and All the subsequent times she appears she looks and acts like  But then she  Well, what if she didn't really? Nicole is the final straw for Isaac as he curses out the marker and. Him being able to shoot at and 'kill' is symbolic of finally letting go of his guilt over not saving Nicole. Then maybe
 * Except that if you let her get too close, she mind rapes you and makes you kill yourself. It's far more likely that she was preparing Isaac for a direct assault on his mind by the Marker, seeing as how the hordes of Necromorphs weren't doing a very good job of killing him.

In Dead Space 3 Ellie and Isaac will be separated at the start.
After the events of Dead Space 2,
 * Then again it's entirely possible that the next game will give Isaac a breather and create a new main character.
 * More likely Ellie will probably be a Co-op player option, much like how Sheva pairs up with Chris in Resident Evil 5. They've already taken a page from Left 4 Dead with the multiplayer, it's not entirely out of the question that co-op will be an option.

There are 'good' Markers and 'bad' Markers
In both games, the two Markers seem to have opposite objectives; one repels Necromorphs and is the key to holding them at bay, the other attracts them and attempts a Convergence Event. But why assume that all these Markers were made by the same people for the same purpose? What if the Marker that stops Necromorphs - the 'good' Marker - was created to stop the 'bad' Markers, like some sort of war with giant chesspieces? The human government is assuming that all the Markers do the same thing, when they're actually unwittingly recreating a war with the left-over pieces. (As to why the 'blueprints' of a good Marker made a bad Marker - remember that the humans are only barely understanding how they work. It's fully possible that during the process of reverse-engingeering the Marker they made a mistake, creating a 'bad' Marker. Especially if you assume that 'good' Markers are modified 'bad' Markers.)
 * I've always figured that the Necromorphs are actually slaves to the Markers, and want to be free. If a marker is unable to control Necromorphs, like when the Red Marker was removed from it's pedestal, they form a Hive Mind to have control over themselves. The reason why the Red Marker wanted Isaac to return it to it's pedestal was so that it could suppress the Hive Mind and gain control over the remainder. It never got the chance to betray Isaac on account of Kendra removing it, and couldn't do anything more on account of being blown up.
 * The problem with the theory of good markers and bad markers is that the Red Marker on Aegis VII is the cause of all of this. Remember, in the first game they talk about the government experimenting with a marker and things going horribly wrong, leading to the complete abandonment of the planet. The Red Marker failed, drove hordes of people insane and created the first Necromorphs (that we know of). No different from the mammoth marker in DS 2.
 * The Black Marker on earth seems to be of a mixed bag as well according to the novel Martyr. The Black Marker also drives people insane who get in it's sphere of influence and also is responsible for a smaller Necromorph outbreak decades before the first experiments on Aegis VII. However it also created a hallucination in form of an old witch causing peasants to destroy a potential Necromorph outbreak years before Altman finds it. So we don't know how close the red markers are to the black one in terms of objectives.

The Markers computers that were made by Intelligent Machines, to prevent intelligent life from forming.

 * The Markers are physical representations of heuristic algorithms. They transmit a signal that causes either mass insanity or visions to cause their replication. The Marker signal causes Necromorphs. The Markers are able to infiltrate the human mind with incredible skill. As one scientist put it, the Markers WANT to be duplicated, and subtly manipulated those around them into doing so. Why? Because a group of intelligent machines, after purging their sector of the galaxy of the "fleshies" decided to make a way to keep them from ever being a threat again. They created the marker, a device that would decimate life forms, yet would inevitably cause those life forms to duplicate them. Convergence events occur when so many bodies reach the Marker that it sends a signal. If the signal is strong enough, the creators of the Marker come to wipe out the "fleshies". And why must the creators of the Marker die? Because the Marker has the same weakness as their creators.

Franco is the Ubermorph
Think about it, In DS1, Doctor Challus Mercer created the Hunter by stabbing a piece of necrotic tissue straight into the head of some poor guy (who was alive at the time). Franco got stabbed by an Infector straight in the forehead while he was still alive. We never get to see his full transformation, and his whole frigging face rips off with tentacles coming out of his skull, whereas most slasher necromorphs have skin on the upper half of their faces. The Ubermorph has those light-bright eye-stalk things on his face, so Franco's face tentacles may have evolved into the glowing facial features of the Ubermorph. The Ubermorph also regenerates, just like the hunter did.
 * Then again, a proboscis to the forehead is the standard infection tactic used by Infectors. Franco's no more likely to be the Ubermorph than any other person.
 * While the hunter was created via necrotic tissue being placed in the brain of a still living victim, it was also implied that this isn't normally possible and only worked because of careful medical intervention by Dr. Mercer. Besides that, pretty sure the slasher blade through the heart probably killed Franco before the Infector got him. Also, the face tentacles are actually a clue that Franco was a secret Unitologist. If you pay attention when you reach the Unitology church, you'll notice that all the slashers are dressed in Unitology clergy robes and have tentacles coming out of their faces. They're also tougher and more aggressive. Religious zealots just make better zombies, I guess.
 * Even in death, the clergy make that hand gesture imitating the Marker - their hands remain fixed that way even if you pick them up with kinesis and bounce them around. (...I was bored, okay?) Since the entire Unitology religion is implied to be the result of the Marker's influence, I would wager that believers are more susceptible to being controlled by it, hence the mass suicides - more material for Necromorphs, more material for Convergence. Maybe that extends to the way their tissue warps as well?
 * If he is, then how do you explain the fact that we kill him before we even reach marker? Or you haven't noticed that necromorph that had same skin color, a flashlight on the shoulder and same clothes, not to mention melted face had attacked you in living quarters? Although it is possilbe that since we kill him even after that, (reusing same skin maybe?) he eventually turned into Uber? Brrr...

The marker only wants sapient creatures.
The birds in the solar array are alive, despite their owner being killed by Necromorphs in the same room. The plants in hydroponics on the Ishimura, in the first game must have had more biomass than all the people on the ship combined, but they were left alone. The markers only want thinking creatures, or humans specifically.
 * Howard (The Watchman for the solar array) actually committed suicide, the Necromorphs didn't get him. Doesn't really disprove the theory, though.
 * However, in Martyr, Altman describes seeing a Necromorphed fish, who was currently attacking other fish. it's possible that the infestation targets only ones that could prove useful to it. In Maryr, fish were the only lifeform available, and would be almost a non-threat to any kind of larger fish. However when you reach the solar array, the birds would be left alone because they are useless to the Necromorphs; why infect a small bird when there are plenty humans around ripe for the taking? It's not like they need to kill them, since when the growth reaches their area they'll just suffocate.

The Marker is a Genesis Device created by an ancient alien civilization to revive their dying race.

 * Think about it: the Marker causes the Necromorph phenomenon, causing dead organic material in it's vicinity to change into Necromorphs. A  occurs when a large number of Necromorphs come in contact with the Marker. Consider this: once enough organic material has been gathered around the Marker, couldn't it just reconfigure all of that organic material into the beginnings of a terraforming system, reconfiguring the atmosphere, biosphere, and ecospere in order to sustain it's original creators? We saw this in Dead Space 1: on the Ishimura, Necromorphs adapted to poison the air aboard to make it breathable. The organic material on the walls is called, in Dead Space 1, a habitat changer. The Markers are a Genesis device for beings so alien that their home environment is one that humans cannot possibly exist in!
 * It'd be a brilliant parallel to Isaac himself: He's just an engineer forced to fight harder than any soldier, whereas the Necromorph threat, which looks like some horrific genocidal bio-weapon, is really just a terraforming tool.
 * But why are the Necromorphs the result? If they're essentially just meat to by malformed, why not just drive everyone batshit-insane and make them go to the Marker via airborne virus, released by the Marker. If the dead species were intelligent enough to make the Markers, why couldn't they just do this?
 * Slave Labor. In both instances of Necromorph outbreaks, we've only seen what would amount to be a vanguard army. The Wheezers seem to be the first signs of an actual, practical application of corpses, but still a practical one, since there's no other reason to have them poison the air, given that necromorphs do a fine job of killing without it, and there's no actual need for them to breathe. The Marker is designed to cause havoc and create a slave labor force, making life easy for it's creators, and hell for anyone else.

The Ubermorph is the original form of the aliens that created the Black Marker.

 * The Ubermorph only shows up once a Convergence event is triggered, if the game is to be believed, and as Marker-Nicole states, Convergence is what the Markers were made for. If the Marker's operating at full capacity and is able to bring forth Convergence, that means it's able to fully complete the Necromorph transformation process- turning Infected into Ubermorphs instead of the 'incomplete' Slashers the Ubermorphs resemble. The Markers might be the alien race's only way of saving their civilization- by re-shaping new generations into more of their own. (All credit for the theory goes to the Dead Space wiki)
 * On that note, the similarity between the Ubermorph and the first game's Hunter may be more than mere coincidence. Doctor Mercer, like everybody else, was being driven mad by the Red Marker; but whereas Kyne was obsessed with studying the Marker itself, Mercer was obsessed with the Necromorphs. Basing it off the theory that the Red Marker wasn't ready/capable of making an Ubermorph, it may have been trying to complete the process piecemeal through Mercer; his attempts to build a better Necromorph may have been a manifestation of the Marker's will to build an improvised Ubermorph.
 * Once again, the Ubermorph actually shows up before the Convergence, it's in the swarm of Necromorphs overrunning the soldiers, and actually, there isn't anything to suggest that Convergence had been achieved. Heading towards, yes, but never fully realized; it's strongly implied that that's why the Marker needed Isaac.
 * Alternate theory: The Ubermorph was some of the biomass sludge aboard the Ishimura; it's mentioned that it reanimates when near a Marker signal; but it would seem odd that somehow it neatly sorted itself back into slashers/leapers/etc. When the sludge was reanimated by the Marker, it built up a construct that, while possessing a roughly human shape, was significantly less human than most other Necros.
 * Ooh I like that theory; the Ubbermorph is infact the remains of the Hunter from the first game, remade by only a particular bit that remained...maybe one the many limbs that Issac shot off. Shame that the last chapters got cut making the end such a mess.

Ubermorphs are nNcromorphs formed from individuals that helped to create a Marker

 * The Ubermorph doesn't show up until one chapter after Nolan Stross dies because it was formed from his infected corpse. The Ubermorph is more powerful and looks more alien than a normal Necromorph because the data and blueprints the Marker imprinted into Stross's mind enabled the infection to transform him into a more "pure" form of alien DNA encoded into the Marker. This is why the Marker doesn't seem to care where or how Isaac dies and continually sends Necromorphs after him the whole game - once he's dead, an Infector will find and transform him into an Ubermorph, and he'll eventually make his way to the Marker and initiate Convergence. (full credit to the Dead Space Wiki for this theory)
 * This is also why the Ubermorph disappears suddenly in the final chapter. The Marker's goal is to absorb all it's makers - Since the Ubermorph is really Stross, once it got close enough to the Marker is was absorbed in preparation for the convergence event.

Dead Space 3 will be all about the Black Marker.

 * From what one can tell from reading Dead Space Martyr and some of the other background material, it seems that the Black Marker was the original Marker and the only genuine alien Marker, the only one that wasn't a replica. And while the Black Marker's ultimate fate- sunken deep within the ocean- is revealed in Martyr, it's never explained what happened to it next. EarthGov might still be trying to find a way to recover it and/or reactivate it. Seeing as Isaac and Stross, the only individuals who came into contact with a Marker, are no longer under EarthGov's control, EarthGov might go back to Earth and recover the Black Marker, if they don't have it already, and in so doing find another way to create Marker replicas.

The stores have matter replicators

 * Nanomachines build whatever item you buy on the spot from an internal stockpile of raw material. This explains all the blueprints you find, all the store needs are instructions and it can build virtually anything you need, you only need to pay for the raw material. When you sell or store items the shop breaks them down for easier storage and pays for the raw material or credits you for the stored item so you can get it rebuilt at any other store for no cost. And when you change your suit, the old one is broken down and the new suit is literally crafted right onto Isaac's body, explaining the swiftness of the change and the bright light and noise during the process.

The Government wants to recreate the Markers to create limitless energy sources.

 * It's actually stated in one of the logs that the research in the Markers was in hopes of tapping into the alien technology in order to use it to solve Earth's resource problems. With the CEC going out of business and Planet Cracking no longer being lucrative, this has forced the government to step up the project considerably. The Markers produce their signal without any visible power source. A device that emits power just by existing could, if harnessed, supply limitless energy for the entire world!

The USM Valor in the first game had necrotic goop in storage.

 * It had some of that goop in storage for one reason or another and proximity to the Marker in the Ishimura reanimated what Necromorphs they were, and as such, the soldiers in the Valor had more to contend with than just a single Slasher. Logs found in the Ishimura do state that something weird happened with the goop they found when they were cleaning it up and it was speculated to be because of signals from the Marker.

All the Red Marker ever wanted was to be destroyed.
Think about it- what is the Red Marker but an incomplete replica of the Black one? The fact that it's red should be your first clue, seeing as it's not supposed to be that way- it's strongly implied that the Red Marker was seriously flawed as a result of being built by humans as opposed to the Precursors that built the Black Marker. Now what if that gave the (sentient) Red Marker the idea that the only way to free itself from its pain was to die?

Pay close attention to what the Nicole apparition (which is basically the Marker's avatar) says during one hallucination: "I'm afraid, Isaac. I don't want to die. But it's the only way out." This is never elaborated on again, but what if it really meant that the only reason the Marker went through its complicated "befriend-and-then-betray-Isaac" because that was the only way Isaac could muster the strength to destroy the Red Marker?
 * If that's the case then why would Red infect Isaac's brain? And later drove bunch of people crazy... again? If Eearth Gov managed to create Red marker, it must mean that they were also infulenced by original right? So how could they go wrong? Unless the reason was in material.
 * The reason is not in the material, but even with the original Marker controlling the Earth Gov people who made the Red Marker, it is reasonable to think that the first time a Marker is made it would be flawed. The Red Marker was a prototype, which is why it was dumped on Aegis VII, and subsequent Markers were better built because the engineers learned from mistakes.

The Hand Cannon allows Isaac to focus and project his latent psychic energy.
We already know he had enough psychic power to blow a skyscraper-sized Marker into rubble. A few Necromorphs should be no trouble, once he had the proper tool.
 * While conducting research on the various test subjects, the team members on the Sprawl found a second, less complex sequence of codes in Isaac's head. The construction that resulted look and felt exactly like foam, and did nothing when anyone else put it on. One clueless lab janitor happened to find it laying around, with a tag saying "Source: Subject Four (Isaac Clarke)", assumed it was his, and loaded it into the shop for Isaac to retrieve later. The Marker gave Isaac such a powerful and uniquely specific tool to ensure he reached the Marker alive.
 * You, sir, just made my day.

Isaac will die in Dead Space 3.
He won't be the protagonist, it'll be someone else. Perhaps he recruited a team to help him destroy a Marker or you just run across him while surviving another outbreak. Regardless, he'll be the guiding voice for you. He'll even occasionally show up like Ellie did and fight off Necromorphs, but then in order to showcase a new deadly Necromorph or even the final boss, you'll get to see him be horribly killed.
 * Right "horribly killed" like the game hasn't already decided that that's the only way Isaac can ever go out.

It's no coincidence that the Overseer shares his title with a rank in the church.
It's either a hint that Tiedmann's boss is a Unitologist spearheading EarthGov's marker research as another vector of getting it done for the church in case their more direct attempts (like Daina trying to nab Isaac) fail, or it's simply a hint for players who didn't read Martyr that Unitology secretly came from the government.
 * It's actually mentioned in Dead Space in one of the logs that Unitology is widespread, even into the political sector, so this isn't that far-fetched.

Isaac is hallucinating all the graffiti in the game.
If I remember correctly, Isaac runs through the same part of the game (either the mall or tenement buildings) twice in the game, but the second time around there's graffiti everywhere. Of course, you might be wondering how the hell did so much graffiti appear in the few hours in between each visit. That's because the graffiti is the Marker messing with his head. Plus some of the other graffiti is just strange and oddly enough seem like messages to Isaac... why would a child scrawl messages like "Mommy is a monster" on the wall? Or a message asking "What would you give up for what you love?" I'm thinking a lot of the graffiti is just in Isaac's head, maybe his influences on the Ishimura subtly bleeding through.
 * Some of it later, maybe, but some graffiti is obviously made by others. Most instances are pretty logical; a child hiding after seeing her mother transform might write "Mommy is a monster", and "What would you give up for what you love" could be written by someone who decided against escaping on a shuttle to rescuing his loved ones. Even the Unitology graffiti isn't too implausible, as they're written in places filled with Unitologists, and in one case you can see the woman who committed suicide after writing some.
 * The only place Isaac revisits is the mall, and I don't recall any graffiti there the second time around. He does visit two tenement blocks and the second one is filled with graffiti, but they're different residential areas, and the second one was close to the church and only Unitologists lived there, so the the graffiti makes sense. That said, he clearly is hallucinating at least some of it. There's graffiti all over the inside of the USM Valor in the first game which couldn't have been real (unless the captain was an undisciplined loon and allowed his soldiers to write on the walls), but most of the graffiti in the games are found in locations where Unitologists were present and going crazy and so was probably real.
 * The only odd thing that can back it up is the fact that some of the graffiti is backwards. Like in a mirror, or even upside down.

The Markers are leftover early Reaper Technology.
They rely on Mind Rape to further their purposes, specifically a sloppier version of Indoctrination. The Necromorphs and Convergence Events are actually early attempts to make the. The Reapers have since found more efficient methods and left the Markers lying around as an afterthought.
 * Fun idea, but not remotely plausible. Humanity found the local Mass Relay by breaking open Charon, Pluto's moon. Given how prevalent planetcracking is, CEC likely would have already cracked open Pluto and it's moon, and found nothing.
 * Pluto doesn't have much in the way of resources, being mostly ice and such. It's also pretty small, about the size of five Ishimuras, so breaking it open wouldn't yield much anyway, as well as completely destroying it. The moons, however, could just be munched up like a twix, a nice little treat. One criticism of the theory, though, Mass Effect's time-line takes place a little before that of Dead Space, doesn't it? If that's true, then the whole theory falls apart, as Mass Effect technology came to the fore on a manned expedition to Mars, and that's the basis for all space travel, so unless there was a complete global disintegration of Mass Effect technology and mass-forgetting of how it works, the theory makes no sense.
 * You're missing the best part of Markers as opposed to Mass Relays - they can indoctrinate in a much more subtle and effective manner. They can literally make the Human Resources make the devices that render them into reaper jelly. Dead Space takes place 50,000 years after the Bad Ending of Mass Effect 3, where the Reapers decided that Shepard got too damned close to wiping them out, and from that point on chose not to give their livestock any assistance whatsoever. Instead, markers were seeded on life-bearing worlds. When species develop enough to uncover their planet's marker, they form Unitologist-analogue "churches" and fuse themselves into the resulting Reaper. Where the Mass Effect galaxy averted "Apes or Angels" via a combination of dead end Mass Relay technology and Citadel conservatism, the Dead Space galaxy lacks alien civilizations altogether - they're all either primitive or have undergone Convergence. The only reason humanity is a spacefaring species is because Altman sank the Black Marker in the Carribean, rather than let the indoctrinated use it to create a Convergence event.

The Markers have multiple personalities
They try to help and kill Isaac, each different approach is a new personality taking control. This is a result of their imperfect nature, being man made rather than alien like the first marker.

Isaac is augmented
Not only did he survive the first Necromorph outbreak but he was (is) the sanest person with that level of marker exposure. He also didn't lose any muscle tone despite being in a straight jacket for three years and can fight some Necromorphs hand to hand.
 * His incredible survivability can be attributed to his Badass Normal factor and Heroic Willpower, and being a CEC Engineer would mean he would have to stay in at least adequate shape. He didn't lose any muscle tone because he was in stasis for most of the three years, only being taken out for a few hours at most for sessions.
 * Not sure about being in Stasis so much, given that you can see Stross being talked to on a log in the hospital.
 * He might be, but that brings up why the soldiers aboard the  didn't survive. If he was, he'd be about on par with an average human surviving the games, since everyone else would be augmented to similar levels to his, so everyone would still be mostly equal.
 * Isaac was lucky. I have a guess (that isn't that wild) that the Necromorphs greatest weapon is surprise. The Necromorph's original infestation of the Ishimura was due to the fact that none of the crew survived their first contact with the Necromorphs. Even if they did manage to survive, the humans wouldn't have any really effective weapons to kill the Necromorphs with. Between a military grade weapon (Pulse Rifle) or a mining tool, which would you use? Probably the military grade weapon, since that is what you would normally use to kill. The crewmen never though of mining equipment as weapons, when in fact that they are possibly the most effective weapon against them. Also, the first weapon that Isaac gets? The Plasma Cutter, something just as efficient at cutting flesh as it is frozen rock.
 * This is proven if you've watched Downfall. The P-sec guards unloaded several magazines into a slasher, but all it took for the big spiritual man was one slice with a plasma saw. Necromorphs are much more resistant to puncture wounds since they lack working internal organs. The entire gimmick of the first game was to break out of the "shoot them in the head" mold of zombie games, Issac was only able to survive because the situation unintentionally forced him to learn about their weakness (he has a cutter, not a gun) while everyone else fled for the security forces aboard their ships, resulting in a less-than-spectacular result (you see the trained guard shoot something, do no damage and get torn apart. A sane man would run the hell away instead of picking up an unwieldy saw and try to go sunday butcher on it).
 * Here's a possibility on why he didn't lose muscle mass. Extended exercise can be very tiring. The people working on Isaac so that he could make the probably wanted him to be as stressed as possible. Being exhausted can be very stressful in certain situations. Constantly pushing Isaac's body to its limit combined with whatever they were doing to him before is probably why he was physically fit enough to stomp off a corpse's limbs. And like the Troper above stated, there is the possibility of Stasis beds.

It is possible to be immune to Marker psychosis
Isaac build up a resistance and Ellie didn't seem to be affected at all.
 * Such a thing is possible. Lexine Murdoch from Extraction is immune, and she's been targeted before by those who wish to study her. Isaac obviously isn't immune, but his Heroic Willpower gives him better resistance from going insane, like Stross did. We don't know if it's that way for Elie, since she never was in close proximity with a Marker that wasn't currently exploding.

The only reason Isaac never killed himself is because the marker wouldn't let him.
This stems from the theory that Isaac's helmet pops off half the time (eg. when Stross tries to stab him in the eye) because he really wants to die. And it makes sense, he's insane, he's been hunted by horrible nightmare-inducing eldritch abominations that look like humans, he's seen a LOT of people die, etc. But then, why doesn't he kill himself? I mean, it's pretty obvious he didn't have anything to live for, before Ellie. And the marker did needed him to get to the site so it could absorb him.
 * If the Marker can stop people from dying, and thus have some control over their actions, why not tell them to go straight to the nearest Infector and take part in Glorious Convergence? And, as well as that, why continue with the Necromorphs if it could control them, and doesn't want them to die? The Necromorphs and people who aren't insane are the only threats they would face, and removing the former would result in the eventual death of the latter from the lack of insane people dying and the lesser numbers of sane people.

The reason Isaac talks so much in this one is because he had taken a recent tongue injury, or had dental work done recently that make talking impossible
In the first game, he's a complete mute, and the people you interact with don't even seem to think it's weird that you don't talk. Well, if he had something wrong with his mouth, something that your two allies were told about, it would make sense he never actually speaks and that neither person finds it weird, and yet is capable of yells and stuff. Actually, with organ grafting (which Dead Space does with cloned organs), it's possible Isaac actually lost his tongue and didn't have time to get a replacement before the DS 1 mission (but did have it capped or something to keep from bleeding), or he had one reattached but it wasn't healed enough yet with the stitches to be able to talk yet. By DS 2, whatever physical condition was causing a speech impediment has long since healed, it being three years, which lets him actually talk this time.

You got to admit, this is a perfect explanation.
 * Also, because of this, it is impossible for Isaac to argue against orders. Why else would he be tasked to fix the entire ship nearly singlehandedly?

The Necromorphs just want Isaac's head.
Issac is almost always decapitated when he fails to escape a grapple with a necromorph, or why he never becomes one of them? This is especially noticeable with the infector death, because it shouldn't decapitate him after finally sticking him with the proboscis. The infectors don't even seem to be injecting him with the infecting fluid, which is shown outside that cutsceen to be messy. Also notable is the leaper death animation, where Isaac's head is ripped off and then immediately dropped. The problem is that necromorphs have not displayed the intelligence or organization to carry something like this out. What they would want with his head is another problem....

The Ubermorph is really Dr. Challus Mercer, The Hive Mind, and the Hunter back from the dead and merged together
however the Black Marker called upon them for a higher purpose and merged them all into an unholy abomination when it brought them back to the world of the living. Now exists the ultimate Necromorph, the Ubermorph. With the Hive Mind's head, thick flesh and the ability to telepathically control and command all the other Necromorphs, the Hunter's ability to regenerate as well as its mannerisms, and Dr. Challus Mercer's appreciation and devotion to these creatures and grudge against Isaac Clarke that keeps him constantly going after him, devising plans with the others to ambush Isaac. He's also invincible as the fan trick might just be a glitch, and we never see him die in the explosions.

Everyone is born with glass bones and paper skin.
This is why you can stomp of the limbs of a person who just died. Apparently, the human body becomes weak in the future, that if you so much as trip, your head and probably your arm would fall off.