Dead Space (series)/WMG

Nicole isn't dead.
During the Necromorph attack of the Ishimura (Naturally after we see her in Extraction), Nicole decides to take her own life so that she doesn't have to live through the ordeal. She sends a message out to Isaac to show how much she loves him, and injects herself with a poison to complete the message of her suicide.

Except that in the midst of everything, she grabbed the wrong syringe. Maybe the Marker was affecting her, maybe she didn't see what the contents of the syringe were, or something else happened; but the end result was that she survived. However, in her unconscious state, the Marker has less resistance from her subconscious and it drove her insane.

The logical extension of this is that in Chapter 7, Nicole really is opening the door, but Nicole is insane due to the Marker. The Hive Mind knew this, and that's why it sent the necromorphs to kill her in this scene. The transmissions of Nicole on the other hand are hallucinations cause by the Marker to get Isaac to trust Nicole. After all, she is giving Isaac the Marker's advice of "make us whole".

Of course, by Chapter 11, she has managed to fight the Marker's influence, just like Isaac did in Dead Space 2. This makes Nicole useless to The Marker, and it chooses the easier option of causing Isaac to hallucinate Nicole and get him to do what it wants. Naturally, this leads to Isaac having to do everything, as Nicole really isn't there. The real Nicole is actually back on the Ishimura fighting for her life, because the marker’s influence is no longer protecting her.

In Dead Space 2, it is revealed that after Isaac killed the Hive mind, the Ishimura survived the planet’s explosion, which means that Nicole is still on board at this point. (Side note: Aftermath shows that Aegis VII also survived the explosion.) The necromorphs turned into the sludge (as stated by audio logs in Dead Space 2), so Nicole doesn’t have to fight to survive anymore, and the Necro-Nicole is a hallucination caused by Isaac being insane as revealed in Dead Space 2.

Dead Space Salvage spoilers ahead:

Earth Gov eventually finds the Ishimura and takes it back to the Sprawl. Since the cover-up regarding Aegis VII is a terror attack, Earth Gov restores the Ishimura to working condition to show the people that they won’t be influenced by terrorists, including installing an escape pod to replace the one that Hammond used to suck out a necromorph in Dead Space 1, which Isaac then later uses to. Of course, a science team is sent aboard to investigate the evidence left by the Marker, because the Marker is a powerful thing.

While restoring the Ishimura, Nicole makes herself known, either by accident or because she heard someone. Someone recognizes that she could be useful in studying the Marker’s influence on people, and Director Tiedemann makes her one of the patients in his plan to save The Sprawl by the research grants supplied by rebuild the Marker(s), along with Isaac and Stross. Since Patient Six from Dead Space 2 is revealed to be female, it would be unknown if Nicole was Patient Six or not. If she was, then the odds of her surviving The Sprawl are nil, given that Patient Six couldn’t "feed, drink, or even bathe herself".

If, on the other hand, Nicole was not Patient Six, then odds are that she escaped from the mental institute where all the Patients were held in the original outbreak, similar to how Stross escaped as well. Her knowledge of necromorphs from her time on the Ishimura, although limited, would be enough for her to make her way to one of the many escape shuttles that left during the evacuation that Tiedemann ordered.

Naturally, the logical conclusion is that it is possible that Nicole is still out there somewhere in the Dead Space universe, though she probably won’t see Isaac again because; A) the galaxy is a large place, and B) the escape shuttles, in the event of an evacuation, would most likely head to Earth where Nicole would be locked back up in an asylum. If the shuttle went to a nearby colony instead, then anyone who was insane (like Nicole) would be locked up, or sent back to Earth to be locked back in an asylum.

Of course, there is always the possibility of Isaac finding Nicole on Earth if he goes there to destroy the original Black Marker, as Dead Space: Martyr says that the Black Marker is at the bottom of the ocean in the wreckage of a research facility that  destroyed to stop the Marker. The ‘Dead Space Game set on Earth’ theory seems probable given that the Black Marker was as damage resistant as, if not more than, the Red and Yellow Markers encountered in Dead Space 1 and Dead Space 2. Of course, Isaac finding Nicole would, on the surface, be a Contrived Coincidence and maybe some Retcon would be required so that it would be believable, so don’t expect it to happen outside of FanFics

What does this mean for the Dead Space series? Nothing really; if Nicole is still alive, then EA Visceral can’t put her into a story since everyone thinks she’s dead. They could probably add some throwaway comments in the Extended Universe that hint at Nicole’s status as being alive without actually confirming anything, but it really doesn’t make that big a difference. It would be a big deal for Isaac, being his girlfriend after all. But since he thinks she’s dead, he’s not suffering from dementia anymore, and Ellie has survived the Sprawl as well, he probably will have moved on by the time we see him in Dead Space 3.

Isaac knew Nicole was dead all along.
When he first got the video, he watched it all the way through. He was sad, but still went on the repair mission to Ishamura because it's his job, and he watched the video continuously out of grief but always stopped right before the end because he couldn't bear to watch Nicole kill herself again. Kendra saw him keep watching the video, but didn't know he already knew the ending, hence her "This time, watch it all the way through" comment at the end.
 * issac IS nichole

Let's face it: Nicole being Dead All Along is not much of a reveal. From the moment she utters the first cryptic "Make us whole again," it's obvious she's not right, and presumably Isaac also has the feeling that what he's seeing isn't right. But nonetheless he can't help but be affected by visions of his dead girlfriend, and he follows her directions because everything the Marker has him do is stuff he was going to do anyway--up to and including putting the Marker back on the pedestal, which Isaac already intended to do before his dead girlfriend started showing up around it as soon as he learned it would contain the Necromorphs.

The Hunter is Jason Voorhees

 * That would explain the Healing Factor, and the fact that it comes back to get Issac personally after being incapacitated the first time.

Issac is a decedent of The Engineer.
This is why, even though he's an engineer, his skill at killing things beats a fully armed warship and his engineering skills specialize in turning things into lethal weapons even though the way he does it doesn't make any sense. His father (or great x a fuckton grandfather) is the Engineer.

Going with the Sliders version of alternate universes, the Necromorphs are an alternate version of Flood.
Sliders states that there is an alternate universe for everything. Dead Space is a universe where the Flood evolved differently and the Forerunners and Precursors never existed (or maybe they did), nor did any alien life seen in Halo. The Flood and the Necromorphs have alot in common (I wouldn't be surprised if they had finished a Halo marathon right before coming up with them). They both use biomass to create forms, they both also use this biomass to transform the walls of a place into a similar fleshy homes, they both are controlled by a tentacled hivemind also made out of biomass and they both have an affinity for turning body parts into weapons. Oh, and Redlight might be another evolved differently version of them.

The Hive Mind and the Marker are competing for control, both sending you hallucinations.
During the scene where you're fighting off the Necromorphs and keeping them away from Nicole, she's opening a door for you. This doesn't make sense, as Nicole is a hallucination and the Necromorphs shouldn't be able to see her, let alone attack her as she's opening a door. But if everyone's a hallucination in that scene, it suddenly makes sense: the Marker's mind-controlling tool of influence is being attacked by the Hive Mind trying to take over. The door was open the whole time and you spent a few minutes shooting a wall.
 * An excellent theory, except that the Necromorphs in that sequence still drop money and ammunition that you can pick up with Kinesis afterwards.
 * Easily explained by Gameplay and Story Segregation.
 * Or, those items were already scattered about, and the hallucinations just incorporate them; Isaac can't see them until he's "killed" the "necromorphs," which then "drop" the random useful stuff they were carrying when they were infected, just like all the necromorphs he's seen so far.
 * Alternate theory: Let's assume that "Nicole" is a physical manifestation of the Marker's influence that only Isaac can see, and that the Hive Mind is vaguely aware of. During the scene in question, "Nicole" is accessing a panel that, in a roundabout way, will lead Isaac to returning the Marker to where it needs to be. The Hive Mind obviously doesn't want that, so it sends necromorphs to take care of it, with maintaining the illusion of Nicole still being alive entirely incidental.

The Marker telepathically took control of Nicole's infected corpse.
And alternative to the above theory. Nicole isn't actually a hallucination, she was infected and turned into a Necromorph after committing suicide, and the Marker, after realizing that Isaac could help it, mentally dominated her corpse to aid him. It uses a normal hallucination to make the corpse look believable and talk. This explains how she was able to physically open a locked door for Isaac and why necromorphs are able to attack and kill her, and is also supported by the fact that a Necromorph with Nicole's face attacks Isaac after the Marker is destroyed, thus losing control over her.
 * With the Hive Mind dead, Nicole should have died (stopped working?) like all the other Necromorphs.
 * That image of Nicole at the end could easily have been a hallucination. Everything else in the theory makes sense, though.
 * In most stories with a hive mind, the death of the hive mind causes the drones to go crazy, entering a rage state, sticking to the last order they were given, defaulting back to their normal behavior, etc. So, the final moment of the end of the game could be the slasher that used to be Nicole just defaulting to "kill mode" or following out its last order: kill what killed us. However, keeping in mind the horrible events Isaac has just survived, the "actual hallucination" theory holds up, too.

Unitology is the evolution of Scientology.
After it faded into obscurity in the late 21st Century, it was assumed that the world had seen the last of it. Many centuries later, it was rediscovered by Michael Altman. Liking what he saw, he decided to resurrect it. With this and the Black Marker, he began the religious movement known as Unitology.
 * Jossed. Dead Space: Martyr tells us that

Doctor Mercer is related to Alex Mercer.
Well, both are related to fleshy, viral eldritch abominations. Of course it makes sense.

Concordance Extraction Corporation, owner of the Ishimura, is a future version of Clamp Enterprises from Gremlins 2.
They both have a similar symbol, at least.

The Twitcher dosen't reverse the effects of stasis
The Twitcher emits a field of stasis that slows down everything around it. It just appears to be fast because it's using stasis on Isaac and any other necromorphs around it.

The Black Marker is Alex Mercer.
Working off of one of the previously listed WMGs, Alex Mercer is the original black marker. Several decades after the events of Prototype, the epidemic created by the Blackwatch viruses has spread to the point where. To combat the ever-increasing epidemic, Alex sacrifices most of his considerable power to seal away the viruses, becoming the black marker in the processes. At the end of Dead Space 2, some government-funded scientists break the black marker, releasing Alex from his inanimate imprisonment and unleashing a viral pandemic on a scale far greater than that of Dead Space 1 or 2. In Dead Space 3, Alex, whose stint as the original marker has made him significantly weaker than his Prototype incarnation, fights alongside Isaac against the new necromorph threat. Accordingly, Dead Space 3's co-op mode will allow both Isaac and Alex as playable characters.

A grand unifying theory
Long ago, the Precursors (whoever they are) suffered from a biological weapon, or created this weapon, which we now know to be the necromorph infection. The necromorphs are engineered to keep their neural cells in their extremities, rather than their main body, and at first their neural tissue remains hidden. But, as they grow, their neural tissue grows into these big shiny yellow things that are exposed to the outside.

In any case, the biological weapon got out of hand, so the precursors then built the original marker - perhaps even a big series of them. Aware that the necromorph infection might take a bit of effort to stamp out, they design the marker(s) to be capable of mind-controlling other species, and putting necromorph DNA in the runes so that people can figure out a cure. Eventually, it was too late so they decided to completely blow up a planet, sending the marker as well as a lot of necromorphs flying. After a few million years, both the marker and the necromorphs land on Earth, and the rest is history. The reason why it seems like the marker(s) cause the necromorph infection is because of the actions of Markoff and his version of Unitology, who only translated the marker symbols that describe the necromorph infection itself without translating anything else and believe it's a way to achieve eternal life.

Also, the reason why the hallucinations seem so disjointed and what not is because the aliens who built the marker didn't know anything about humans, much less how their brains worked, and thus the marker's mind control is... let us say... inefficient.

Another Crazy Theory
The markers are pure evil. It's the pedestals that are good, and which are trying to prevent the infections.

The characters you play as in Extraction have vestigial twins growing out of them, or perhaps an extra set of limbs they aren't in full control of.
In two-player mode, characters only ever refer to you as a single person, and there's never a mention of anybody that could be considered a Player 2 following you. despite how there's two guns being used, two damage bars, and each side gathers ammo separately. Either you have a vestigial twin with two hands that can use guns, but is still considered just 'you,' or you have four hands, but the other two aren't fully under your control. Fortunately, they do want to live just as much as you do. Separate health bars indicate enough damage to that portion of the body to incapacitate it.

The infection is centered in limbs and buboes because each Necromorph is a miniature version of the Hive Mind.
Rather than take over a subject's nervous system, the infection creates its own system connecting the subject's limbs via numerous redundant channels made through the victim's body. Just as the Hive Mind is stronger the more Necromorphs it controls, individual Necromorphs are more durable the more limbs they have to divide amongst. Pulping the body destroys the connections between limbs, but this isn't as efficient as simply lopping off arms and legs to disrupt the mini-hive-mind. Likewise, in more powerful Necromorphs, while the body becomes insanely durable due to other effects of the infection, the infection centers become bloated and comparatively quite vulnerable. Most Necromorphs simply keep those limbs out of the way or guarded to become basically unstoppable. Issac seems unusually capable of goading these weak points into the light because...

Issac is The Chosen One.
The reason most boss Necromorphs are dangerous--outside of the Slug--is because they don't flash their vulnerable members when Issac isn't around. Issac has been chosen by the Marker due to possessing a rare genetic marker/psionic sensitivity/unique strength of character/incredible willpower/a higher power is invested in his survival. Either: he exerts psychic influence on boss Necromorphs that compels them to expose their weak bits, only he can see where the weak points are and take advantage of them, only weapons in his hands can actually lacerate a Necromorph's weak points, or his presence offends more-intelligent Necromorphs so profoundly they are compelled to beat him to death with their own nerve systems.

Dead Space is an alternate Mass Effect universe.
Think about it, an alien relic found on Earth that was theorized to be within the asteroid that wiped out the dinosaurs. It has a hidden DNA within its coding that when applied to human flesh, it turned them into monsterous abominations. The relic itself keeps these creatures subdued within the confines of its 'dead space'. A man-made attempt at this relic only made the effects worse, this particular copy also causing hallucinations and madness within the living. Can anyone say "indoctrination" yet?

Let's face it, if we suddenly saw Turians or Krogan blasting their way through the Ishimura coated in Necromorph spew, we wouldn't be half surprised.

Isaac is a Wood Elf, or at least a Half-Human Hybrid of such
How else does he manage to stay so clean, even when being showered by blood and guts from the Necromorph he just killed and walking over (and stomping on) rotting corpses? He has to have that Elven "Forcefield of Cleanliness" thing going on!

Dead Space takes place in the past of Warhammer 40k
The unupgraded pulse rifle being the weakest weapon in the first game is an ancestor of the lasegun,and the marines in the game ,their entire ship and crew getting killed by one slasher are the ancestors of the imperial guard.The marker was made by nurgle to spread the necromorph disease.

Dead Space 3 will have references / shout-outs to John Carpenter's The Thing out the wazoo. Bonus points for a parody of the blood testing scene.
Rumors so far say that the main setting of DS3 is a planet completely covered in ice and snow. I'd honestly be shocked if they didn't do this.