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This is a "Wild Mass Guess" entry, where we pull out all the sanity stops on theorizing. The regular entry on this topic is elsewhere. Please see this programme note.
Prototype
All Evolved and Runners are made of some sort of organic metal.
That could explain their immense durability and how they weigh a lot.

Alex Mercer is a long lost relative of Desmond.
Mercer has a preference to wearing (imitating) clothes with a hood, he is a master class parkourist, he is a master of infiltration, and even the Blackwatch troops usually fail to recognize him lest he does something high profile. The Templar must be pissing their pants right now.

9/11 was only half successful in this universe.
There is a place that LOOKS like ground zero... with one tower (the spire one) and another one being built (or, should I say, rebuilt) in the game.
  • This is pretty much confirmed in-game; one of the Web of Intrigue videos has a pilot talking about shooting down a commercial airliner.
    • Except that's a soldier shooting down an airliner trying to flee New York due to the infection. Pay attention.

Dr. Challus Mercer from Dead Space is related to Alex Mercer the original
Apart from the surname, both of them are involved in research to turn normal people into monsters. Maybe Alex left a secured log that would be found and decrypted a long time later by a distant descendant The Hunter regenerator is merely a stepping stone in Challus's attempt to recreate the powers of Alex Mercer the player character. It would be... fascinating if the True Final Boss of the Dead Space sequel was a Captain Ersatz of Alex Mercer the player character. Oh wait, crap.
  • Why would he need to be a descendent? A change of face and name are quite simple for Alex. Besides, it's not like he will ever age.
  • However, Isaac Clarke is pretty capable of punching out Cthulhu. The battle could go either way. As for the theory; both Mercers do share a disregard for even basic human decency, so it may be possible Challus is real, non Virus Alex's great-great-great-etc-grandson, assuming sociopathy For Science! is a genetic trait.
    • Well, if Isaac spammed the stasis module, while constantly blasting Alex with his higher end weapons, then yeah, he has a chance. However, stasis is his only chance — most of the Necromorphs were incredibly slow in comparison to Alex, and once Alex gets into melee range with the blade, it's over. More on topic, one wonders if Isaac is in some way related to Cross — two Badass Normals who routinely take down apparently much more powerful Body Horrors?
    • DS's Dr. Cross obviously never inherited the badassery of Cpt. Cross.

The Blacklight Virus was created by Umbrella.
  • Zombies? Check. Giant, horribly strong mutants that can kill armored vehicles? Check. Horrible rapid combat mutations? Check. Hell, Alex Mercer's abilities aren't all that far from what the Uroboros does to Wesker at the end of Resident Evil 5.
    • Alex is what Wesker wishes he was when he grew up.
    • Or, the Blacklight virus was engineered based on Uroboros recovered from Wesker's body after the Final Boss fight of RE5.
      • No, the body would have been immolated eventually. The plane with Uroboros, however, could have been recovered.
  • No, it doesn't fit, at the time of NY outbreak Wesker's still alive, well and hiding and Uroboros isn't done yet. Anyway, they are from different uneverses, otherwise the fight between Mercer and Chris (who became a worcaholic after Jill's death) would be inevitable and one of them would be killed in it before Prototype2 and RE5 - temporal paradox, people.

One strain of the Blacklight Virus is the cause of the Zombie Apocalypse of Left 4 Dead.
  • Hordes of lesser infected, with smaller numbers of more powerful ones? Hell, it's like Alex Mercer has superior versions of the powers of several of the boss infected. The smoker's long range grab (Whipfist), but Alex is faster reeling them in. The parkour of the hunter, but Alex is even more agile and can leap much further. The strength and resilience of the tank, but much faster. The claws of the witch.

Two more strains of the Blacklight Virus were used on the Toguro Bothers
  • Something was done to them after their Dark Tournament win to make them powerful "demons". There is plenty of mad science going around, and at least one instance of, you guessed it, superpower-giving parasites. So it's entirely possible that the orchestrator of the Dark Tournament could have had access to the Blacklight Virus. This version of the virus does not bestow all of Alex's powers, but the ones they do have are enhanced. Further proof can be found by looking at their powers. The Younger Toguro clearly has a souped-up Muscle Mass power, and the Armor power, though it manifests as tough gray skin rather than beetle plates. He only has two powers, but the level of enhancement goes way beyond what Alex can do with those same powers. The Elder Toguro has... pretty much everything else, honestly. He can shapeshift, he can extend his limbs to attack (whipfist), he can rip things to shreds with his nails (Claw), he an transform his limbs or whole body into a sword (blade), shield (shield), and many other things besides. While both brothers can regenerate, his regenerative powers are so advanced that he can survive total point-blank annihilation, just like Alex. And for the final piece of evidence, look here. Go ahead, look at that and try to tell me that it's anything other than the Tendril Barrage Devastator. Elder Toguro even gains the power to eat people later on, for crying out loud. It doesn't get any clearer than that, does it?

Prototype 2 will feature Alex Mercer versus an army of homicidal cyborgs and robots powered by nanomachines.
The Infected were kind of taken as far as they would go in the first game. Also, Prototype usually refers to a machine rather than a biological entity. Also, a Robot War is the only thing that could possibly challenge Alex at this point, since he'd be unable to feed on them to gain health. Also, since he's not such a maniac at the end of the game, letting him constantly eat random passer-by would be kind of a Snap Back, so the solution is obviously to have them all replaced by killer robots. Cyborgs would also be able to get the drop on Alex, pretending to be regular humans until they bust out the giant freaking laser beams and missiles.
  • Jossed as of February 2011 gameinformer.

Plus, who wouldn't play a Prototype game in which you were Alex Mercer versus the Matrix and Skynet at the same time? Possible with lots of sequences of Alex fighting Sentinel-like giant robots. Also, dividing the enemy factions into Human Military, the Infected, and Machines would inject a lot of much-needed diversity and some other playable characters if need be. And thematically, pitting a protagonist who is a giant mass of shapeshifting biological components versus a nanomachine monster would work like a charm.

Alternatively for Prototype 2: Aliens
Jeeze, when you've got a character as powerful as Alex, the only things that would slow him down are Sufficiently Advanced Aliens and a cross between the Terminator and Mecha Godzilla.

Cole MacGrath from inFAMOUS is Pariah
With the theory that Alex Mercer is the Beast, why not? They don't tell you about Cole's past. He could be a 'recovering amnesiac' and not know of his past as a test subject who somehow escapes. And since he stopped using his naturally born abilities due to it, they began to wither away (apart from the ones that can't be explained by electricity, perhaps, such as his enhanced endurance and impact falling), before getting a jump-start via the Ray Sphere, or in Kessler's case, figuring them out at some point (explains how he got his abilities in the future). The main problem with the theory is that from what has been seen, the virus' abilities have been biological. But since Pariah was suppose to be the 'next step', electricity may well be Humanity's next evolution!
  • OR! Pariah could be the Beast. The Beast seems to have fire based powers, so it may not be Alex. And then sometime in the future, both Cole and Alex fight Pariah/the Beast in a cataclysmic battle of epic proportions, full of erupting volcanoes, lightning striking from the heavens, and great feats of strength and skill unlike any seen before.
  • ...That has to be one of the best ideas I've heard, excellent! That probably means, however, that in Kessler's time, Mercer was killed before they could team up. Doesn't explain some of Cole's abnormalities. But hey, there are other explanations...
    • Easy. Redlight and Blacklight are 2 of 14 (or was it 15) strains of virus. Cole has one of the others, maybe called Bluelight or Whitelight.

The Supreme Hunter is the parasite that was injected into Mercer by Cross.

Theory formed by the Web of Intrigue piece from Dr. Jared Cooper. In it, Cooper talks to Cross about the parasite injected. He claims "we're supposed to be stopping these things, not manufacturing new ones!" The final scene is the Supreme Hunter standing over Mercer. This also explains why the Supreme Hunter is not only intelligent, but able to shapeshift and use quite a few of Alex's attacks. It's also a good degree more human-looking than the rest of the Hunters. Too close for coincidence in my eyes.
  • That's not a "theory", that's pretty much canon. During one of the cutscenes, the soldier Alex is talking with, who we later discover is Specialist Cross, who we later discover is the Supreme Hunter even says something in the lines of "A sentient cancer parasite. Do you have any idea how he felt being torn away from his host?". Mutant parasitic cancerous vengeful biological abomination with daddy issues? Yeah...
    • The only point of uncertainty is: did Alex inject Elizabeth Greene with the parasite removed from himself (or some part thereof, it seemed to have grown far too large to fit in the injector), or more of the same material Cross originally injected into him? In any case, it is most certainly the same type of parasite, just with a different reaction to the Redlight virus.

Alex Mercer has an organic quantum storage device.
Otherwise, where does he keep all of that body mass? In fact, with all the mass you've devoured even after the first mutant fight, you should be able to create any possible form he could think of.
  • He keeps all the new mass inside his own body, thus becoming super-dense. That's why he plummets in water like a rock, stops cars that crash on him and wrecks them in the process, and crater-lands after a jump.
    • Also notice all the clouds of red when Alex does things and uses powers, that's him disposing of extra mass as well as burning it up, so he stays at his "crack the sidewalk when falling" weight.

The game is actually an FPS in which you play as the boss
Think about it. It's pretty much a straightforward apocalypse scenario shooter, only the twist is that you get to be the horribly difficult recurring big bad of the game.

CUSTOMARY NGE THEORY INCOMING: Mercer And Greene Are Angels
Let's see the check list: 1. Eldritch Abomination: A horrifying voice from Beyond says "Check." 2. The Juggernaut when it comes to non-Angel based weapons: Walks in, mildly sunburned. 3. Bizarre Biology: Tentacle slides out and gives visual approximation of thumbs up.

My theory is that Blacklight is in fact a culture of cells from Adam, which still remain somewhat sentient. As a result, the transformation of Greene was actually them realizing they had found a suitable host for transformation into a humanoid Angel like Tabris. After possessing her, she then gained the ability to created pseudo-Angels in the form of the Infected-the reason they have a Hive Mind is that they're really just one big Angel. When Mercer-the human one-enhanced the culture to make them more powerful, he really caused the original Angel to become two. The new Angel/cell colony tried to possess him but only succeeded in making him drop the vial. However, by that point, they had become powerful enough to mimic his form, as well as a human mind. They-or rather, he-then was driven by instinct to destroy the "weaker" Angel-the Infected. He succeeded, and then went on to his true purpose at the end of the game-finding Adam's body.

Where does the original cast of the series fit in? They don't. It's an Alternate Universe in which the Second Impact wasn't nearly as bad as in NGE.

  • Or, taking into consideration Pariah is called the purpose of all life and Greene stated she was "the reason for everything" just before Alex triggered the Supreme Hunter's birth, then think of Greene and her son as the combination of Lilith's and Adam's descendants: Humans from Lilith, virus from Adam. We still remember what happened during Third Impact? Adam + Lillith = God. Or at least something with a god-like power. With that power, Shinji was able to re-shape all life on Earth, most likely revived Asuka and everyone else became LCL, people finally left him be and Asuka was with him, tadaa. That "re-shaping life" part should sound familiar. We got three persons that are working hybrids: Greene, Mercer, Pariah. Now we don't know much about Pariah, but we know Mercer's shape-shifting abilities on a genetic level, his ability to re-write living organisms, his consuming abilities, and Greene's abilities to create Hunters and an Infected army in general. Sounds pretty much like the ability to re-shape life to me (Also, Mercer is called ZEUS, hehe, pretty god-like in itself if you ask me).
  • The Angel that gets WTFPWNED in Asuka's Rebuild 2.0 intro scene certainly has variants of Groundspike Graveyard and Tendril Barrage.

At some point while rampaging around the City, Alex accidentally absorbed the powers of The Prince of All Cosmos
Doesn't his people-eating powers make him look like some kind of corpse-katamari? (He doesn't get any bigger because of his Hyperactive Metabolism.)

Semi-obligatory Warhammer 40,000 theory: It's not on our earth but a facsimile created by Chaos.
Alex has the Tzeentchian shapeshifting, the Khornate martial prowess, and the Nurglite virus thing. Slaanesh... may fit in there somewhere. So he's a prototype for some Chaos super-warrior meant to be superior even to Chaos Space Marines, but the ending shows he's not quite willing to go along. If there's anyone with the slightest shadow of a chance of Punching The Big Four Out, it may be Alex with the power of lots (and lots and lots) of consumed (greater) daemon (prince)s.
  • Slaanesh is easy: Tentacle Rape Overdrive.

Cross is Pariah
Cross repeatedly shows that he can fight on even terms with Alex, yet is presented as a normal human (albeit with years of military training and the best equipment the military can give him), which seems a stretch, given that Alex could easily crush normal humans with 1 or 2 blows, regardless of armour (Alex can crush tanks, what makes the military think any kind of personnel armour would stand a chance?). However, if Cross is Pariah, it explains a) what happened to Pariah: Blackwatch kept him and raised him as a son b) how Cross is capable of fighting Alex on even terms (he's got a similar virus boosting his abilities) and c) Cross becoming the Supreme Hunter: during Cross's last stand, his Redlight powers awaken, and starts fighting like Alex to survive. However, consuming that many Infected causes Cross to connect to the Redlight hivemind, and he fills in the blanks as to his past and what Blackwatch did to his mother, thus causing him to betray Blackwatch, and willingly consume the Supreme Hunter (or possibly let himself be consumed by the Supreme Hunter, though it seems unlikely that Elizabeth would let her only son be consumed by the Supreme Hunter).
  • Unlikely; it's mentioned in an WOI that Elizabeth Greene is "imperfect", Mercer is "something more", and that Pariah could be "the final purpose of all life on Earth", and it would be a very, very bad thing if Mercer and Pariah ever came into contact with one another. If Cross was Pariah, why the Hell would they send him to fight against Mercer, if in their own words it would be even worse than Mercer is by himself? Hell, why even let Cross walk around if he's "the final purpose of all life on Earth"? As for how Cross can last more than one punch; I'd say gameplay and story segregation.

The Final Boss of Prototype 2 will turn out to be Dana
Maybe Dana was too horrified by Alex's true nature or found out that he wasn't really her brother, and decided to work with the government against him. Or maybe she was infected in the first game and so has joined forces with Pariah to fight Alex. Either way, Alex will be forced to kill Dana, the only person he ever really cared about in his existence. The loss and betrayal of his Morality Chain will lead to Alex's true Start of Darkness. Then he will embark on a path of destruction across the globe that, in one timeline, claimed Cole Macgrath's wife which will lead him to become Kessler, and cause people to name Alex The Beast.

Alternative Warhammer 40,000 Theory: Blacklight is a Tyranid organism.
We know that the virus itself is sentient, and it works in hives. Its only discernable desire is to consume. It creates horrifying biological nightmares with lots of claws and tentacles. It can assimilate human DNA to shape new organisms. This all fits the criteria for a Tyranid attack, but one more subtle than even genestealer cults, which may have been involved as well. The virus itself is Tyranid, and the original Alex Mercer was a genestealer hybrid who intentionally awakened Blacklight because he sensed an incoming Hive-Fleet. The "Alex Mercer" you play as is in fact a Synapse creature, controlling and directing the virus' infection of the world-the virus itself exists simply to have the world ready for immediate consumption by the Hive-Fleet upon arrival, without bothering with open warfare. Hives form Capillary Towers, the planetary biomass is absorbed, and the Hive-Fleet moves on.
  • What would that make Blackwatch then? A powerful Radical Inquisitor's private army?
    • Not necessarily. It's entirely possible that Prototype's Earth is simply a world out of contact with the rest of the Imperium and has come to think its the real Earth. Blackwatch could simply be exactly what it appears to be-a black ops section of the military with extremely questionable ethics.
  • Why does Alex fight the infected then?
    • Hive fleets have been known to fight each other. Maybe whatever work Gentek did on Redlight means that the main swarm doesn't recognize Alex as one of their own anymore.
  • Another possibility: Alex is captured and shot into another galaxy via a secret government project FTL-capable spaceship. Approx 40,000 years later, Hive Fleet Behemoth shows up...

Alex becomes New York's superhero
Admittedly a horribly destructive and violent one. But after realizing how much he cares about Manhattan, he uses his powers to take down organized crime and the like.
  • More like he becomes New York's Guyver. Powerful, destructive, inhuman, and capable of killing hordes without a thought, yet still better than the alternative.
    • Come on, you know Blacklight would make an awesome codename.
  • He would make a damn good Nineties Anti-Hero.
    • Only what kind of ungodly powerful supervillain would be needed to pose a threat?
      • Physically, Alex is very powerful, but actually no more so than a lot of middle-tier superheroes - Superman could probably take him to school, for instance. Also, threats don't have to be lone supervillains; they can be conspiracies, impersonal forces, natural disasters, all kinds of things. And Nineties Anti Heroes often have no worse an enemy than themselves - which goes particularly for Alex, a creatures whose goals in-game, protecting humans and destroying the infection, run contrary to his very nature. He has ten thousand voices in his head continuously screaming in agony. If you can't make a plot out of that, you just ain't trying.

Blacklight contains Spiral Power or a corrupted version thereof.
Tendril Barrage Devastator looks really like the Giga Drill Maximum. The Whipfist's grabbing action is reminiscent of that time Simon and Yoko took Gurren Lagann webslinging drillslinging along flying Ganmen. Gurren Lagann even gains its flight pack by assimilating another Ganmen, for goodness' sake. His is the Devastator that will pierce the heavens?
  • Not quite:
    Mercer: Mine is the Devastor that consumes the heavens!

Alex is the original Bydo
Both are manmade Creatures of Mass Destruction produced from human tissue, with the ability to corrupt their surroundings, against which the only useful weapon are modified versions of themselves. The original data must have been used as a basis for developing a Planet Killer some time after the events of the game.
  • Alternatively, Alex ends up creating the Bydo when the Strogg invade Earth.
Blacklight is an Alternate Universe G-Unit
Well, the Armor upgrade looks like G1, and taking over Alex's dead body/appearance could be seen as an equivalent to taking over for Sho in the fight with the Enzyme. That's... all my evidence. I just thought it'd be pretty cool, and make for a good crossover.

Alex will take control of the remaining infected
It seems pretty clear to me that the Blacklight infected have some sort of hivemind given Elizabeth's ability to control them, and with Alex being the only Blacklight creature with anything resembling intelligence left, it follows that the remaining infected might look to him for some sort of purpose. With the Dana plot thread left hanging, chances are good that she's been infected as well, so that would provide a good hook for Alex to want to take the infected under his wing.
  • He outright states that he's the last possible leader of the Infected to Cross/the Supreme Hunter.
  • But after the plot is all done, the infected are just as hostile to him as ever.

Blacklight is Seed
The only real difference between Alex and a Deadman is the blood transfusions (and even that isn't such a big difference - Alex still needs biomass, after all).

After the game, Alex learns from some of his acquired memories that the next highest ranking man at Blackwatch is one General Shepherd and ends up rucking it with the 75th Ranger Regiment searching for him.
Copy / Pasted shamelessly from the Modern Warfare WMG page: Okay, so there's a government conspiracy afoot, right? Shepherd was secretly involved in the BLACKLIGHT project as well as his own scheme. When he went to recruit Allen, Mercer snuck in and consumed Corporal Dunn, proceeding to infiltrate the Ranger battallion in hopes of getting to Shepherd. Unfortunately, they Rangers were transferred back to Virginia shortly before the Russians attacked, so Mercer, still trying to maintain his cover, played the role of Dunn. Think about it, how many times have you seen Dunn take enough bullets to kill you twenty times over, and still get up? Immediately at the start of Second Sun, he takes a bullet to the shoulder and isn't impaired in the slightest. As for why he doesn't just use a devastator or start tearing Tanks apart barehanded, since the events of Prototype, he's trying to be focused more on the "heroic", less on the "sociopath" part of being a Heroic Sociopath, and doesn't want to needlessly slaughter the Rangers (Let's assume Dunn was part of Black Watch before transferring to the Rangers, so he had it coming).
  • Alternately, Dunn wasn't Blackwatch, he was actually perfectly innocent; Alex acts scared shitless as Dunn because that's how the others expect him to act, it's part of his cover. Dunn was mortally wounded in combat and was the first such soldier Alex both found and was able to consume as a Mercy Kill without anyone seeing; this actually gels well with Prototype canon, which suggests via character development as the game approaches its conclusion that Alex (aka, Blacklight) is growing out of his Sociopathic Hero phase. In order to learn how to act like him, Alex would've had to have absorbed him fully with his memories intact instead of pounding his brain into paste; Dunn displays a sudden bout of patriotism after retaking Whiskey Hotel when another Ranger expresses a wish to counter-invade Russia because in taking Dunn's memories, Alex inherits his desire to serve; Alex could also wish to make up for the horrible things the real Alex Mercer did, and once someone else kills Shepherd, presumably crippling Blackwatch, sticking it out with the Rangers would be a convenient way of doing that.

The personalities of the people Alex consumes continue to exist inside his head.
The thousands of people he's consumed are all aware and capable of communicating with each other, and Alex, who hears them as a sort of endless Inner Monologue he can't control. No particular reason other than it would be really cool.
  • Isn't that basically canon from the last cutscene/conversations with Cross?
    • Nope. Alex recalls everything that happened to his victims as though it happened to him, including their horrible deaths at his hands (hence the screaming in his head. That would obviously be the clearest and most recent memory). In the WMG, that would be because they're still alive, but in canon they aren't; the voices are just echoes.

The sequel will star a new Runner: Dana, with Alex serving as your boss.
This would bypass Alex's current Physical God status, letting us control a Runner starting from the basics like Alex was in the first stages of the game and thus make fighting the military/infected an actual challenge.
  • Well, she would be... popular with the net.
    • Addendum. Alex will have transformed her so as to save her from being a regular infected. This will explain any differences in powers.
    • The comics show that there is a confirmed Runner that escaped Blackwatch, and they don't know about her. It's Garcia; you see her all crazy like at the end of issue 6.
  • Half-right, half-wrong it seems. Turns out Alex is likely to be the boss, but the new Runner is just some random grunt.

In the sequel Alex (or alternate player character) will have a Bio-Gun.
Seriously, who hasn't though how cool it would be to shift one of your arms into an organic cannon, firing bio-mass (possibly draining health) or taking the bio-mass of living enemies and using that as ammo. Did someone say Civilian Cannon?
  • He can already shoot biomass with the Critical Pain devastator.
    • Yeah, but that's a Devastator and you really can't make consistent use of it. Imagine having something like the Slam Cannon in Generator Rex only fueled by people. How awesome would that be?

Prototype is a Marvel AU
Specifically, this is an altverse origin story for Venom, as he develops from murdering sociopath to Anti-Hero of New-York. Alex shares many properties and powers with Venom, shape-shifting, Combat Tentacles and strongly associated with the color black. The Supreme Hunter is Carnage, sharing several of his powers, being born from a piece of his flesh, and having a red theme to contrast his black.
  • Alternatively, Alex managed to find a way to summon a ForbiddenBeast, the price he paid was his memory. He doesn't experience the decomposition Eddie does because he can renew himself with additional biomass.
  • The Marvel theory is lent additional credence by Spider-Man: Shattered Dimensions; where Ultimate Spider-Man (wearing the symbiote suit) shares quite a few similarities with Alex in terms of attack animations, and Ultimate Carnage fights sort of like a combination of Greene (He spends a lot of time inside a fleshy, tendrilly blob; and the people he drains to husks turn into Carnage-allied zombies) and the Supreme Hunter (Out of his blob, he uses groundspikes, claws, and tendrils)

The virus was based off of DNA found in a fossilized alien crash site in Antarctica.
Body Horror, Paranoia Fuel, Voluntary Shapeshifting, enough said, right?
  • Furthermore in the video game, it's revealed that the covert military group headed by Colonel Whitely was doing extensive (and unethical) research into possibly weaponizing The Thing (which they classified as the Cloud Virus). Whitely's group could easily have been a predecessor or a part of Blackwatch.

The Prototype Sequel Will Take Place in Las Vegas
Makes sense, the place has plenty of cool looking buildings that light up well. The surrounding deserts can justify the army's ability to enforce a quarantine by artillery strike. But the main reason would be to deploy this image to maximum effect.

The random blonde killed in the cinematic was Karen Parker.
This is the PG-rated version of a theory I found on deviantART.
  • Jossed by the game. If you find all of the Web of Intrigue nodes, there's a short cinematic of Alex infiltrating Karen's safe house and killing her (well, terrorizing her, but c'mon — do you really think Alex Mercer is going to stop at scaring her?).
    • You don't get a Web Of Intrigue node, though, and the game specifically cuts out before the whole Consuming thing begins. Given that by this point the player has devoured probably at least thirty people to finish the game's missions, I'm not sure why it would decided to censor that unless it was going to be a plot point. I mean, some of the Consume animations involve shoving someone's head inside their ribcage. Seriously?
      • Personally, I am inclined to believe that Karen is still alive, but I just wanted to mention a possible counter-argument to the "fade-to-black" thing. Yeah, there's been a ton of violence and bloodshed up to that point, and a ton of it afterwards — however, that scene, to me, was about psychological horror rather than visual. It really played up on Alex's ability to be anyone, anywhere, without a single person knowing. The game definitely shows it, but that scene really jacked up the paranoia level for me. Personally, if he did kill her, I think that simply fading to black, with the player knowing exactly what's going to happen to her, is more horrific than simply being shown the same kind of murder-consumption we've seen a thousand times before. In short, Alex could very well have killed her, and the fade out was just for dramatic effect.
'Nother minor addition: Karen Parker never wanted to betray Alex in the first place. Given the Web of Intrigue nodes that feature her, I get the impression she was strong-armed into working for Blackwatch and GENTEK against him. At the very least, two nodes that feature Blackwatch operatives mention that she's wanted for "questioning", and the one where she's actually being questioned and admits that she doesn't know where Alex ran off to features a shot of a Blackwatch soldier's memory: him standing over a handcuffed/tied-up woman with bruises all over her back. The woman in the shot is blonde with short hair, just like Karen.
  • Also, I can't think of many better ways to fake someone's death than having it seem like they've been completely devoured by Alex Mercer... No need for a body, after all.
  • According to the section of the official strategy guide that includes commentary by the creators, Karen is dead:
    Parker's Character Bio: Parker uses Alex's memories of her and his fragile emotional state to keep him in check, something which becomes more and more difficult to achieve as time goes on. Parker is interested only in saving herself, and understands Alex's odd predicament fully; she knows, for instance, that "Alex" is dead, and that the virus has replaced him. As such, she is both amazed and repulsed by the creature she is forced to work with. Eventually, that fear will cost her life.
  • I'm doubtful of how canonical the strategy guide could be considered.
    • Honestly, so am I; but it's the 'bonus' section where the Dev team, rather than the writers of the strategy guide, talk about the characters, their roles, and their development (along with some really badass art) as well as their profiling. So I'm a little more inclined to believe it. Trust me, had the bit about Karen just been thrown in the guide somewhere, I wouldn't have bothered to post it. *fistshake* I've been lied to before.
    • I know that, I'm still doubtful. Strategy guides are compiled before the game is finalised and sometimes contain inaccurate or out-of-date information, and aren't necessarily canon sources even with developer comments. ...Plus having to beat the shit out of someone to make them work for you doesn't mean they count as "willing".
      • True. Didn't think of that. Also, in regard to Karen not having a choice... Yeah, I agree totally. I hope that Alex didn't kill her, because she really seemed regretful while speaking to him — ("For what it's worth... I'm sorry that it had to play out this way.") — and GENTEK/Blackwatch twisted her arm when it came to betraying Alex. "Betray the virus who took over your ex-boyfriend's body and we'll give you any assignment you want, with great pay and flexibility, and pardon everything you've done wrong thus far, or... well, there's nothing we can do for you." Considering Alex's transformation into a being with actual morals (and, presumably, a capacity for mercy), I would like to think that he spared her.

The Guards aren't actually all that crazy...
Okay, so the random Marine and Blackwatch mooks seem not to notice the player character clearing buildings in a single bound, running at cheetah speed, etc, but do seem to notice when he grabs someone/attacks/or has his blade/claws out; nor do they recognize Alex without a disguise, even though he's been (correctly) known as the terrorist behind the outbreak. My theory is that this isn't due to them not noticing the other stuff, but because they don't want Mercer noticing them. Think about it, if he runs past them, leaps over a wall, then continues forward, then those soldiers are the luckiest bastards in Manhattan at the time; they escaped Mercer's wrath. Shooting at him would only piss him off, chances are they'd be dead before backup arrives. So therefore, the Guards do notice all the crazy hyperparkour, however, they don't want to open fire (unless Alex is so flagrantly using his powers that it's clear he's going to kill them anyways), hoping that he'll just ignore them.
  • It could also be a case similar to the "How could guards not notice Sam Fisher's glowing NVGs?"
  • While I agree with the troper below me, the thought that they're just ignoring Alex crossed my mind, even though they ran to the craters. After all, they do have to acknowledge that something just happened; they don't have to acknowledge that they know who's responsible for what happened — at least, no one can prove that they saw who did it. Sure, there's a guy who resembles Mercer, maybe, I guess, who happens to be wandering around near the crater — but that could just be any dude, right? We should just investigate the crater. And if no one's specifically at the crater, I guess there's not much we can do, huh?
Mercer is clearly visible for the player to control him properly, but is actually incredibly difficult for humans to see, maybe it's some sort of minor camouflage caused by the virus, that only dissipates when he attacks, or gets too close. Jump off a very tall building, break the pavement. Notice how the Marines/Blackwatch will run to the crater, and not your character?

Average citizens know Alex isn't the one to be afraid of.
Sure, he can (and, depending on the player, does) absorb and eat anyone he wants, most of the time the average citizen sees him destroying Hives, obliterating hordes of Infected, and single-handedly absorbing beasts that would eat them as a snack. While they are naturally still afraid of him, they don't think he's in the area to ruin them.
  • ...Er, I think that might depend on the person. Most people, myself included, would probably scream and run. Even if I did figure out that Alex was only specifically after the Infected and the people crazy enough to open fire on him, I don't think I could see him as anything other than just another monster. I mean, I don't know anything about the guy. If he grabbed me out of the way of a tank, or struck up a conversation with me, and then went off and starting killing Infected, then maybe I wouldn't be so concerned about him personally. And yet I'd still run upon seeing him, because where Alex goes, explosions, gunfire, and death are sure to follow.
  • Actually, come to think of it, in the comics, it's explicitly stated that some people do think Alex Mercer is ripping up Hives and beating the crap out of the Infected, so... hey, he might not have too bad a rep after this. Not quite 0% Approval Rating, anyway.
    Radio VO: Social messaging website have provided the best coverage from inside the city; there are reports of Alex Mercer ripping apart the Infected. Many feel he may be the key to combating the effects of the virus. Others insist he's somehow responsible for the outbreak.
  • God bless you, Facebook / YouTube addicts. May your vigilance never falter, even in the face of a Zombie Apocalypse.

In the Next Game The Military Will Have A Do Not Engage Protocol For Alex Mercer
Sending in troops just gives him food and guns. Sending in Tanks just lets him hijack a tank. Sending in Air Support just lets him fly around in a gunship. So if there is a sequel, the military will adopt a policy of not attacking Alex unless he attacks first. Even then, they will try to run. This will result in the crew of tanks abandoning it the moment he jumps on top of the tank, and helicopter pilots ejecting out so he doesn't kill them, with humorous dialogue. Pilot: "You want it, it's all yours!"
  • Except that there's no way to get out of the vehicles before Mercer turns the helpless crew into red paste. The animations even show tank crews desperately clawing their way out of the turret only to get yanked back in, and helicopter pilots struggling to jump out rather than be killed by Mercer.
    • Well, they could always start putting gigantic, bright messages on the sides: WILL BAIL OUT, PLEASE DO NOT EAT, HAVE LEFT SANDWICHES AND BEER IN COOLER
  • More likely, the military could just rig their gear to explode when Mercer gets inside.
    • And potentially blow themselves up? Sure, you could probably rig a minor charge into the controls to make it scrap on wheels, but that's a recipe for misfires and wasted tanks. You're really better off just letting Alex have one.
      • And it's not like Alex isn't capable of doing more damage on his own than with a tank anyway, depending on what he's attacking.
    • Or they avoid sending in ground forces and let the air force handle it. Alex would have trouble hijacking a b-52 in flight.
      • I dare say that sounds like a challenge.
      • It would only take a small upgrade to his superjump-airdash-glide combo to turn it from Not Quite Flight to Real Flight.
      • Or consider this, since Alex is basically an insanely dense clump of biomass that weigh possibly in tons, it is not impossible for him to just dedicate some of that mass into processing power far beyond what little brain we Muggles have, then it won't be far-fetched to say he could snap-calculate everything he needed to accurately shoot whipfist to catch that B-52, the rest is just chomp-chomp or however it is he eat, and maybe how to get close enough to it to pull it off

Mercer is an Assassin
He has insane acrobatic skills, guards ignore him until it gets violent, and he changes into other guys like the guys in Brotherhood's multiplayer. Need I say more?
  • There is actually a little interesting fact here: You can actually see a logo that reads "Templars" one some of Blackwatch's equipment in the cut scene.

In the sequel Alex will lose all his powers after being in an hibernation state
After Manhattan events Mercer will go into a near coma state to know himself, loosing most of his powers but getting into a tabula rasa to learn new ones, getting a new default look (It's also the most acceptable way to get a fresh beginning for the game I can think of). I imagine a large forgotten underground bunker, in the deepest chamber, a small room contains a human sized flesh egg sustained by tendrils firmly attached to the walls, inside just a biomass, a slow almost unheard beating. Several years passed and finally a crack appears, but nothing comes out, instead the whole egg starts getting form, a human form, hands, hair and even clothes take form from the mass, something stands out where the egg was, sometime called Zeus, called Blacklight, called Alex Mercer. Not human, less than human, more than human, its objective unknown, its past a merge of things, its present....survive. (I should write a fanfic with it)

The World is an Alternate DC Universe
And Alex is Superman. Take a look at another alternate DCU, and tell me you don't see the similarities.

The new player-character will be a cyborg created by the military.

Come on, by this point, Alex Mercer is a frakking GOD. The military (Or blackwatch) would probably have to do a simple "Fight fire with fire" policy, by making a cyborg to fight him that runs off humans. The upgrades would be you being literally taking apart by the military and having new stuff added. Plus, you could pretend to be human by just switching to non-lasers and metal oh my mode.

Come on, you'd play it. And plus, Alex Mercer could be running around whatever new city or county or maybe country in real time, and you could try to stop him!
  • A cyborg wouldn't be a believable opponent against Mercer. He can crush tanks. No cyborg would remain functional long enough to do the job.

Cross isn't dead.

I am calling this one right now, since I don't see them throwing away a character so casually after taking so long to build him up. For one, we don't SEE him get consumed in the cutscene, which as mentioned in the Karen Parker issue seems highly suspicious indeed, though slightly less so than the aforementioned example. Secondly, we don't know how powerful consuming is or at least how far it can go. Do you have to eat the entire person in order to impersonate them, uniform and all? Could it work with just a hand or other disposable body part? And Cross may be mortal, but he IS still Dangerously Genre Savvy. In Prototype 2, he will be back sans one natural arm (which he cut off in a Randellesque attempt to escape) and more dangerous than ever.

The Blacklight Virus is related to Cthulhu.
It will devour all of humanity. Just not all at once.

Prototype takes place in the world of the Cthulhu Mythos.

  • The Blacklight Virus is not actually a virus. It is a seed of the Old Ones that humans have managed to weaponize, without realizing what it is. This explains why Blackwatch is so psychotic and crazy, and also explains why they've gotten crazier in the second game, to the point of outright villainous insanity rather than excessive devotion to the job. The entire storyline, from the destruction of Hope to the way New York ends up in the second game, is all part of a very subtle long-game plan by the Old Ones, since their more outright stuff involving cults has failed so often throughout the 20th century. The Blacklight Virus is a tool designed to seek out the most powerful potential servants, and they've used it before. Both Alex Mercer and James Heller's abilities are very similar to what Nyarlathotep is said to be able to do in the Lovecraft stories. This explains how the Virus can make them defy the laws of physics. The scientists spout something about biomass because it's the closest our understanding of the world can get to explaining it, but the virus actually makes the protagonist into vessels of the Old Ones, pulling power and energy directly from the Outside where they are locked away. This explains why Alex Mercer went from a very dark anti-hero to a full-on A God Am I villain. The Old Ones corrupted him and drove him mad, just as they do to all things of this world when they come into contact with it for too long. James Heller seems more resistant to their influence, perhaps because he has his daughter to fight for. If they ever make a third game and he ends up the villain, it'll show that the corruption eventually won out.

To Glide, Mercer....
  • Converts some of that extra mass into something akin to Kinetic Energy. It would explain why he keeps falling even as he glides, despite the fact that he should be far FAR too heavy to fly while he has a human shape and significantly higher density. The reason this doesn't effect His health is because It would take a HUGE amount of energy to actually kill his mass any. Might even be part of the reason they call him Zeus

  • Creates Gas filled Sacks in his body that make a gas that is MUCH lighter than air. Considering the amount of people he's eaten if he gets their knowledge and what not in full, It wouldn't surprise me if he figured out the physics of it. As to the gas made...dunno

  • Shoots out millions of microscopic tendrils out to the nearest buildings to lift or support him, dragging him down slowly instead of dropping him like a rock. Explains the boosting (he's pulling himself forward)

  • Shaves off bits of his mass in order to become more aerodynamic.

This is a Prototype2-teaser
I mean, what else should this be?
  • Plot speculation, go! Alex is after the real leaders of Blackwatch, possibly the Templars as mentioned above, while being pursued by (insert threat: Blackwatch, PARIAH, other unnamed Infected, Blackwatch and their brand new pet Infected). Where he goes in this quest, destruction inevitably follows, and you, as the player, will have the option of controlling how much destruction is caused in your choice of powers and methods - do you infiltrate, precise and careful, or tear apart everything in your way? Dana returns either as Alex's data analyst (and having taken a level in badass) or slowly dying/going nuts from her infection while Alex searches desperately for a cure. Or both. Setting: ...I have no idea, but I hope it's not just New York again.

Alex Mercer will be a decoy villain in Prototype 2
  • Your real nemesis will end up being Pariah, and that's what that big monster thing is in the final shot of the trailer. At least I hope so...I don't want Alex to die.
    • Me neither. But, on the plus side, Alex survived a fucking A-bomb, he won't die by the hands of some stinking new Player Character. And I also don't think that we get to consume him because, well, that would be a little lame (although pretty ironic).
      • Alternately, James get eaten halfway through the game by Alex, letting you control Alex for the remainder of the game.
      • As a Third Option, James ultimately, in his single minded revenge, jumps off the slippery slope into villainy, perhaps allowing himself to be assimilated into the Redlight Hive or something for the prospect of getting revenge on Alex, and ultimately becomes a menace that its up to (ironically) Mercer to stop.
  • They might do a "play as one or the other" type-thing. Choose from the start to play as Alex or James. Either that or you rotate between them.
  • They might end up working together when James Heller learns that Mercerlight isn't the real monster.

There will be a shocking twist for James Heller
Just look at what the twist for Alex Mercer was in the first game. Something about the new guy isn't going to be what we are initally told.

James Heller IS Alex Mercer
  • More specifically, he's the chunk of Mercer/Blacklight that we saw at the end of the first game. Having to regenerate From a Single Cell did a number on Blacklight's already jumbled memory, so the only identity it was able to hold onto was that of a random soldier Mercer absorbed. Heller may have jumbled memories of his own death at Mercer's hands and may have come to the mistaken conclusion that Mercer infected him, when in reality he was just outright absorbed.

James Heller IS a part of Alex Mercer
  • After being blown up to pieces, a part of Alex consumes James while he was still alive, so that part ended up being "James", while the other bits of Alex only consumes animal or dead bodies so they don't develop into another Runner. And at the final battle against Pariah or someone else James will be consumed by Alex voluntarily to stop The End of the World as We Know It or something

James Heller didn't exist as a person, but as a melting pot of soldiers Alex absorbed in the first game.

Alex is a Time Lord.
Because someone had to say it!
  • No, but he might have eaten one at some point.

An earlier attempt at releasing was tried in Hawaii...and thwarted.
  • Sometime in 1969-70, a scientist working on a deadly microorganism, which turned out to be a modified form of the "Hope, Idaho" strain, grew disillusioned and stole the sample from Fort Detrick. Eventually arriving in Hawaii, he intended to release it on the entire State as a lesson on the horrors of bioweaponry. That is, until the local Five-O managed to both calm him down and helped track the sample before it could be released. The Army detachment sent to clean up the mess presumably destroyed the evidence. But the poor doctor's research is salvaged to create the Blacklight virus down the line.
    • And in case you're wondering, it's based on an old Hawaii Five-O story arc involving someone disturbingly similar to Alex Mercer (pre-virus).

Prototype exists in a universe that has superheroes.
It explains why, when Alex is leaping over buildings, Marines say "Fucking New York!". They've probably seen footage of Spiderman, Peter Petrelli, or any other New York-based superhero. As for why said superheroes never show up, they're either dead or in hiding.
  • Or know damn well that bad things would happen if they get eaten by Mercer, and stay outside the quarantine zone.

Heller will ally with Mercer at the end of the sequel.
  • After learning of the true evil (Pariah and the governments actions) Heller will then either allow Alex to consume him, enabling Alex to gain a massive boost in power.

If there is a third game, PARIAH will be the main character.
Because, why not? Also, spoilers ahoy. I think it would be fun to play as a Creepy Child. I think he also sounds more like a Woobie, Destroyer of Worlds to me so maybe the plot will be centered on him trying to escape where ever Blackwatch is holding him to either a) find his Mother b)Find Alex Mercer because he killed his mother/Alex is looking for him/some other reason, c)To find out what the hell is going or d) Find Dana Mercer if she turns out to be a runner. There is also the whole dealing with infected everyone/everything you touch but it'd be cool if you could command small armies of infected or use a hunter as transportation. Maybe there'll be new infected even!

The main villain will be Alex Mercer.
No, not that Mercer. The original Mad Scientist Mercer survived, and in the end Heller and Virus Mercer will team up to take him down for good.
  • But then how did he survive getting riddled with holes and devoured by his own virus?
    • The most likely method would be that when they touched in the station, the virus got his form and he became infected in a similar manner to Heller. I also just find it weird for our Mercer to be Playing with Syringes, and I wouldn't be at all surprised to see a fake Alex in play.

Karen would be appearing in Prototype 2 as an ally to James Heller and Blacklight-Alex.
However, the latter would still be angry at her for betraying him even if it's possible that Blackwatch forced her to do it. Later, she makes a Heroic Sacrifice when a virus monster is about to eat Alex, prompting a Tear Jerker scene of him finally forgiving her for betraying him, and she knows that it isn't Alex forgiving her, but the virus.

Heller will kill Dana Mercer in Prototype 2
Three probable ways this could happen:
  • Dana obviously knows a lot about Alex and what's happened to him, and she's also one of two people he really seems to care about (Ragland being the other, debatably). Consuming Dana would be a big Web of Intrigue boost for Heller, and would also give him a form he can take to get close to Alex without raising his alarm. Of course, once Alex finds out what happened, then it's game on.
  • Elizabeth Greene knew Alex would kill her, so she deliberately infected Dana to make her the new hive mind. Since there's no way Alex could bring himself to kill his own Living Emotional Crutch, it falls to Heller to do it.
  • The viral outbreak in New York killed Heller's family, and he shows extreme hatred towards Blacklight-Alex. So he might simply track down the comatose Dana and kill her just so Alex feels his pain.

The Supreme Hunter survived Mercer's attack on the USS Reagan and will return in the sequel
The giant monster featured at the end of the first Prototype 2 trailer certainly looks a lot like him, doesn't it? And If Mercer can rebuild himself From a Single Cell after a nuclear blast, then the Supreme Hunter can probably recover from a bunch of stabs and cuts given that it's on a ship full of people to consume. It even has aircraft the Supreme Hunter could use to get back to New York.

PARIAH is the reincarnated Alex Mercer.
Think about it: after he is shot to death by Blackwatch and the virus took on his form, Elizabeth Greene has managed to get a sample of his blood and inject it herself.
  • Jossed by the fact PARIAH is older than Alex.

Heller will team up with Alex in the middle of the game.
Maybe while fighting, he'll find out that whom he is fighting against isn't really Alex, but it's the virus who begins to have a conscience.

The sequel will end with Heller performing a Heroic Sacrifice.
He doesn't want to live anymore now that he has avenged his family. As a result, he blows himself up with the virus, so that New York City is a safe place again.

Alex will still be playable in Prototype 2
The game will be split into two campaigns, one is Heller, the other Mercer:
  • As the Trailer showed, Heller releases the Virus back into New York, injecting himself with a sample directly into the veins and causing a different, but similar form of the virus to create him. He goes on his Roaring Rampage of Revenge to kill Alex for not killing him.
  • Alex's is based around surviving Heller's wrath, finding out how the infection started up again, who James Heller actually is, and then fighting him when he kills Dana to mess with Alex, instigating the coolest and most deadliest boss fight EVAR.

PARIAH is Hulk.
Well, the main personality of his is being an immature child who destroys stuff, and he is responsible for Leader, Abomination, She Hulk, Red Hulk, A-Bomb, and Red She Hulk.

Dana will become a runner in Prototype 2.
Elizabeth Greene said that "she's with us now", Dana will become a monster just like her brother is.

The entire game is a Dying Dream.
After the real Alex Mercer unleashes the virus at Penn Station and died there, he is placed in a dream as punishment for his actions. All the characters in the game represents his conscience for redemption.
  • Himself = Ego/Self
  • Elizabeth Greene = Id
  • Captain Cross = Super Ego
  • Dr. Ragland = Anima
  • Supreme Hunter = Shadow Archetype
    • Dana'd be more likely to be Anima, since that's the female aspect of the male soul in Jungian psychology. ...Just saying.

Mercer infected Heller for a specific purpose.
Mercer, by the end of the game, wouldn't want to cause the kind of damage involved in a Redlight/Blacklight outbreak without a damn good reason. One possibility is that Blackwatch has yet to be exposed, and he started another infection event to bring Blackwatch's indiscretions to light. Another is that PARIAH is still at large, and that Mercer is doing this to draw it out, using Heller as a decoy while he closes in on it.

Heller is a Villain Protagonist
People keep mentioning how Alex infected Heller, and how he's had a Heel-Face Turn, but in the trailer for Prototype 2 it never mentions that Alex was the one who infected him or that he was the one who released it. I mean, why would he? We saw that Virus-Alex cares for Manhatten and wants the stop the virus. The answer is: He didn't. The trailer specifically said that Heller wanted to die and Alex didn't let him, what he means is Alex stopped the infection, Heller didn't get the chance to die and now wants to kill Alex for it. So how do you kill an Elderith Abomination like Alex? You even the playing field, it was Heller who re-released the virus, not Alex, and turned himself into a runner so he could kill Alex. Alex has likely been using his powers for good since the end of the last game.
  • Unless the developers are lying, this has pretty much been Jossed by the various interviews and previews they've released. The virus wasn't re-released, it's the same outbreak from the first game only it's gotten worse over the 14 months between the games. The developers have explicitly stated that Mercer infected Heller on purpose and have even released concept art of it.

Mercer infected Heller for a damn good reason.
Heller complains that Mercer didn't let him die. Perhaps Mercer discovered him dying and decided to infect him to save his life. Unfortunately for Alex, he saved a Death Seeker.
  • According to the Prototype Wiki, this is correct. Mercer found him dying and injected him with Blacklight to save him.
  • According to interviews he infected Heller because he wants to make Heller his lieutenant in "a plot to spread the virus beyond New York Zero".
  • Which interviews? This Troper has only found the actual trailer, the various teasers, and one interview which just says 'he[Alex] sees that Heller has potential'. The spoiler tag isn't needed BTW.
    • The EGMi (EGM's online magazine) interview. It's also mentioned in the article for the print version of EGM.
      • Link Please?
      • EGMi (it's in issue 246.2).
      • I Stand Corrected. I part is now disapointed that Mercer is indeed the villain, but another part is sure that there will be some kind of twist revealing the truth, can't know until the game actually comes out though. This still gives me many different WMG about the plot though.
  • It stil seems that Mercer has a reason for spreading the virus. It could be a gambit to draw out Pariah, or more of Blackwatches higher ups. And what better way to draw attention then with TWO extremely powerful super humans?

If there is a third game, Alex Mercer will be a playable character.
This game will be a prequel, and I'm talking about the real Alex who is a sociopathic monster. The storyline will start from his rise to Gentek to his death by Blackwatch in Penn Station.
  • A completely ordinary if sociopathic biologist watching microbes in petri dishes and filling in reports. Sounds like fun. I can't wait to see you try and pitch it to Activision.

McMullen is a G-Man.
It is possible because he knew everything about Alex Mercer by just manipulating him into making the virus. On the top of that, he even knew his disguise as a soldier.

ZEUS pulled a legitimate villain turn
With so many theories about Alex faking the evulz, I figure somebody should put forth a couple as to why he actually might be the villain of the sequel. First might be a not-entirely unfounded disdain for humanity. From the moment he woke at the morgue, people have tried to kill and manipulate him; the list of people he can trust is pretty much nonexistent. He intimidated Ragland into helping him out. He trusted Karen Parker, and all he got in return was a sentient cancer parasite. The person who stood best to humanize ZEUS was Dana, who is understandably not in any position to help him.

Making things worse is the fact that he's flipping nuts. Really, ZEUS was not a nice guy; he was the lesser of three evils. Even assuming he wasn't merrily slashing his way through civilians like players were, look at who he's been consuming to get information on the Web of Intrigue; members of Blackwatch and Gentek researchers. Having them in his head would likely give him a dim view of humanity. Add on to the fact he has Greene and Randall in his head. Both were involved with the virus from the beginning; and both likely have very divergent views, which both believed were the one true version of events. Having them both in his head can't exactly bode well for his long-term mental health.

Finally, there's the fact that he is the personification of a horrific death virus. As much as he might regret that fact, he knows that he was designed to be a deadly plague, nothing more or less. So directionless, having no one to trust, with a head full of enough crazy for a small country, and the knowledge that he's nothing more than a mad scientist's successful attempt to make a deadly plague even deadlier, and it's not that hard to believe that at some point within the fourteen months between Prototype and Prototype 2, he reached a Despair Event Horizon/Eventually lost his marbles from everything/Decided "screw it, Being Good Sucks"/What have you.

With that accomplished, what does Alex decide to do? Why, the same thing any viral abomination would. Raise an army of infected monstrosities, and take over the world, of course!

If there is a third game, James Heller would be the playable character.
This is between the two games showing how he fights in wars, he has to leave his wife and daughter for a war from the overseas.

The ending of Prototype 2 will be the death of Alex and Heller
The final mission would be the boss fight between Alex and Heller fighting against the real Alex Mercer, the creator of the Blacklight Virus and the one who unleashed it to New York. The first part will be the real Alex using his much more powerful virus powers. After being defeated, the second part will be him doing an One-Winged Angel as he transforms into the giant monster virus. Being outmatched, Virus Alex has to have Heller be absorb so that he could be more powerful. Being a Death Seeker for a long time, he allows that, and Virus Alex gains the power of tendrils and Biobomb ability. He faces his creator and wins. Unfortunately, because the real Alex could get more powerful in each defeat, Virus Alex self-destructs himself to kill him, bringing peace to New York City.

There are three campaigns in Prototype 2.
The third and final campaign will be Alex and Heller realizing that their fight triggers the presence of PARIAH, Elizabeth Greene's son, trying not only to avenge her death by the former, but also to rule the world. The two would have to team up for this.

Blacklight has not pulled a full face heel turn.
When Blacklight regenerated at the end of the first game, part of it split off and reformed a seperate body, giving Blacklight its first Hive Mind. Blacklight, realising the potential in this orchestrated a massive plan involving the virus spreading beyond New York to draw out Pariah while Heller keeps it from becoming to wide spread. In order to save her life, Ragland infects Dana with a different strain of Blacklight which ultimately strengthens her, making her the "cure" to the Redlight Virus. Blacklight will spread the cure, Heller makes peace with Blacklight realising why he did what he did, Pariah will be killed by being infected with a specialised parasite created by Ragland from Dana's blood. Prototype 3 will feature a Supreme Hunter type Big Bad which was caused by the Cure and Pariah coming into contact.

If he is truly being infected similar to Heller at Penn Station, he would have been hiding in the shadows planning something that could cause The End of the World as We Know It.

The Blacklight Virus is based on the Alpha Worm.
Body Horror? Check. Giant monsters? Check. Carriers? Check.

Prototype 3 will be about Dana.
After hearing news of her brother's death, she woke up from her coma to investigate it.

Predictions for Prototype 2.
  • Alex will still be playable.
  • The final battle would be in the rain.
  • The ending would be the death of Alex and Heller.

If there is a third game will be about a new virus and stopping a new military force.
Somehow, some scientist of Gentek stole a sample of the Blacklight Virus after the aftermath of the second game and turned it much more deadlier than 10x. That scientist ended up infecting himself with it before he allows himself to be shot to death by the military. However, he returns to life trying to stop a new military force worse than Blackwatch.

The third game will be about a new virus trying to be a hero.
Going with the WMG above, he will do favors for everyone in New York, gaining him popularity.

James Heller is PARIAH.
You see, his fate is unknown during the first game. It is assumed that he is adopted by the Heller family and is named James. He grows up to be a happy adult with a wife and daughter until he lost them to the infection. When he becomes infected by Alex, it reawakened his memories of what he is and his mission: to destroy Alex Mercer for not only the death of his adopted family, but also the death of his mother, Elizabeth Greene.
  • This is interesting, but I have a bit of an issue with it. For one, PARIAH is a white six to eight-year-old kid. Even if you say that he can change form, then James loses his sympathetic motivation. Plus PARIAH can't grow up. He's the son of Elizabeth Greene, and she hasn't aged a day in 40 years.

There will be two endings for Prototype 2.
Based from the theory above, "Alex will still be playable in Prototype 2":
  • Heller is about to kill Alex, but he manages to escape his wrath.
  • Alex absorbs James, and proceeds to fight against PARIAH. However, he does a Taking You with Me move by self-destructing himself, saving New York City.

Alex is a Death Seeker.
Has been in the sequel, and maybe that's the reason he becomes a Rogue Protagonist.

James Heller will be a Decoy Protagonist for Prototype 2.
The real protagonist is Alex Mercer, despite of becoming a Rogue Protagonist. I get the feeling he infected Heller just to make him strong enough to absorb him.

Heller will take control of the Infected.
I don't see why not. He's a soldier by any chance, so what?

Alex will be playable near the end of Prototype 2.
Near the end, James has defeated Alex, but he gets absorbed by him. As a result, Alex is playable for the remainder of the game, gaining the tendrils and bio-bomb.

Heller really is a Prototype.
Specifically, Alex is trying to alter all of humanity into becoming something like him, and is using Heller as a Prototype. He's probably doing it so humanity can survive PARIAH, or the infection in general.

Alex is a Well-Intentioned Extremist in Prototype 2.
I just have my reason of why he becomes the villain. It turns out he wanted humanity to keep on living.

Alex infected Heller to become powerful.
Maybe the boss fight with him is to test out his powers if it succeeds his. Once that is done, he absorbs him, finally becoming more powerful than ever.

If there is a third game, it would be about a female virus.
In two games, we play male viruses, so why not try a female one? It's possible it could be Dana or any other female.
  • It's rumored that Activision's management generally refuses to cast females as protagonists, due to allegedly poor sales of games which do feature women in the led role.

Elizabeth Greene's absorption by Alex is all part of her plan.
As far as I believe, she wanted Alex to absorb her, and thanks to that, she will take control of his body during Prototype 2.

The ending of Prototype 2 will be a Genocide Backfire.
It would be about James finally reconciled with Alex and team up into destroying the remnants of the Blacklight Virus being unleashed in New York City.

James Heller is the protagonist all along.
Playing as Alex Mercer in the first game would be the background. It should have started with a normal man having a normal life until his life falls apart by something. For James' case, it's the death of his wife and daughter. As for his origins of his powers, he joined Blackwatch to fight the virus, but it's because he wanted to die. However, Alex infected him with the Blacklight Virus, giving him the powers he has.

Heller is a manifestation of Mercer's conscience.
He is created representing his sign of doing good deeds since he's a soldier fighting for a cause. He will disapprove of his actions of spreading the infection.

Heller is going to be much worse than ZEUS.
Okay, Zeus started out with the moral fiber of a sociopath, and gradually developed some empathy, and care for humans, despite bieng the manifestation of a horrible killer virus. So you can somewhat excuse his horrible actions. Heller on the other hand is a human to begin with. How are you going to excuse his eating 9000 innocent people a day?
  • Gameplay and Story Segregation. To be honest, if in-story Alex did a quarter of the things I did to civilians throughout the gameplay, he'd be way past the point where his actions could be "somewhat excused". YMMV, but I find a Roaring Rampage of Revenge for the deaths of one's family a more sympathetic motivation for charging headlong across the moral event horizon than "I have no memory and want to figure out what the fuck's going on, and am sure that one of the people I'm angry at is responsible for all my problems".

Heller will kill Zeus.
I mean straight up, dead and gone. Consume him with no chance of coming back. And then he'll find out it was some horrible mistake.

PARIAH will become The Antichrist.
His fate is unknown during the first game, so I've been thinking about this theory. It's possible he escaped from Blackwatch by using charisma on a soldier to let him out and infect the other soldiers. If he ever shows himself to New York, he would appear as an attractive boy with good publicity and leads everyone into following him, resulting in their deaths by infection.

Prototype 3 would be Alex vs. Alex.
If the real Alex comes back as a virus being, it's a possibility.

Heller will unknowingly spread the virus around New York.
He has the power of tendrils, right? What if this is the power used to spread the virus even more, even beyond New York Zero?

PARIAH will be raised in Kinderheim 511.
He's already an Enfant Terrible when he's captured by the military. If it's possible, he'll be worse than Johan.

Alex Mercer was once an orphan for Kinderheim 511.
Have you noticed he is evil while his sister Dana is good? After he decided to go foster care, he is placed through various orphanages and one of them is a military-theme designed to turn children into heartless monsters.

The ending of Prototype 2 will be "The End of the World as We Know It" kind.
Alex's plan is to spread the virus beyond New York Zero, right? Well, it looks like James has unknowingly have the power to spread the virus even further in his adventures rather than just stop it. Way to go, James.

The events of the first game is a book written by Dana Mercer.
Curious about her brother, she has decided to write down everything he does in the whole game. Well, Ragland will help her finish it when she is comatose thanks to Elizabeth Greene.

Heller had a history with Mercer before the infection.
I wonder, two researchers working together on the Blacklight Virus? Soldiers from a war? I don't know.
  • Highly unlikely. Mercer was a scientist who had little experience with military hardware prior to the game. Heller presumably has no scientific background.

BLACKWATCH was created by the SCP Foundation.
you know its plausible.

While hunting Mercer, Heller will have an Amnesiac Dissonance.
Stay with me, people. Based on some theories, "Heller will kill Zeus" and "Heller will be worse than Zeus", it's possible there are some hidden secrets that Heller may be oblivious of.

PARIAH is Damien Thorn.
His mother is Elizabeth Greene, but his father is not shown or reveal. Maybe his father is Satan, having impregnated Greene before the infection. This makes PARIAH not only get his virus powers, but also the power of being The Antichrist, explaining the glowing eyes in a Web of Intrigue.
  • PARAIAH's father is implied to be a hippy shown in the Prototype comic mini-series. And PARAIAH's eyes aren't glowing in the Wo I, they're just scribbled over like various other people in the Wo I including a doctor in one of the Super-Soldier nodes.

The Blacklight Virus is created by the Chimera.
It's their backup plan in case they fail.

The Agent is a prototype for the Supersoldier.
Related to the above WMG. At the end of the game the Agent is an absolute hulk who can clear buildings in a single leap. Qualities similar to those possessed by the Blackwatch Supersoldiers, who are the only human (well, humanoid) mooks who can rival Alex Mercer's abilities. Like the Supersoldier, though, the Agent still isn't quite a match for Mercer. He can't run along vertical surfaces, for one thing...
  • Even more so in 2. The Freaks are humans mutated by a virus, who slowly progress from basically zombies to giant apelike monstrosities covered in pus. Maybe Czernenko was experimenting with a different strain of Blacklight (ability to spew acid, but vulnerable to sunlight)?

Prototype is the sequel of darkSector.
Alex Mercer and Hayden Tenno are one and the same.

If Alex is also the protagonist of Prototype 2, then he's a Supporting Protagonist.
It focuses more on Heller...

The events of the second game is a book written by Alex Mercer.
To keep track of Heller's progress before confronting him directly.

Heller will be better than Mercer.
Stay with me. He is a human, right? A human with virus powers. His motives are happen to be more heroic, despite of the killings he has to do with the innocents. If he stays on the right track, he's better than Mercer.

The Blacklight Virus has a similar case to Mitochondria Eve.
Somehow, before his death by Blackwatch, Alex has transferred his files about his work to Dr. Hans Klamp. He has instructed him to infect someone with the virus to a perfect and that is Maya Breda. The next instruction is to implant donors to two individuals who will carry on the infection if Maya dies: Aya and Melissa.

Meaningful Name: Blackwatch.

Alex Mercer is a prototype of a T-1000.
The release of the Blacklight Virus by him before his death by Blackwatch has created this time loop: the entire world is taken over by the virus. One of the T-1000s attacked the resistance, but John Connor has managed to contain it. Thinking it might be useful, he has reprogrammed the T-1000 and model him to be like Alex to stop the threat. He did serve his purpose in the end of the first game, but with no purpose in the second game, he goes back to the original programming: spread the virus.

Alex Mercer was actually a Carnage-style symbiote that was killed/poisoned/mutated when its host was exposed to the Blacklight Virus.

Prototype is a Deconstruction of superhero video games.
I got this idea from playing this game. Judging the way this game goes, it's different from all superhero genres; the superhero you've been playing all this time is an Eldritch Abomination who attempts to reclaim his memories and revenge. However, the thing is he kills people to get what he wants; he absorbs them and took on their forms to get to that person.
  • Perhaps a deconstruction of sandbox games, full stop? After all, no matter what the story says, at some point in any sandbox it's inevitable the player will get bored and start massacring the local NPCs, and there is rarely anything in the story to justify or punish the character for acting that way. Enter Alex, who is enough of a psychopath for that not to matter - and then make the key plot revelation that he's not even human. Because really, what sort of bastard would act that way, even if they had the ability...?

The Mercer bloodline is cursed to suffer great misfortunes.
Let's start with their father; he's not shown, presumed it's a Parental Abandonment. Then their mother, who only appears in Alex's life before another abandonment. Alex himself is only a pawn for Blackwatch and gets murdered by them, but not before he unleashed the Blacklight Virus. Dana, on the other hand, is one big sufferer by the hands of anyone, including Blackwatch and Elizabeth Greene.

Ragland did something to Dana when Alex assigned him to watch over her.
And the sequel would reveal what that is.

The Blacklight Virus is a descendant of The Darkness.
Well, an ordinary virus can't just have superhuman abilities. There must be a source of it.

The Blacklight Virus has the power to resurrect the dead.

If Heller fights PARIAH, he won't enjoy it one bit.
Even discounting the fact that many people would feel revulsion at having to kill a kid, Heller used to have a young daughter. Having to kill PARIAH may even make him realize that he and Alex are Not So Different after all.

Karen Parker was working for the FBI.
Considering how evil Blackwatch is, it's not possible for the FBI to take an interest in it. They need to get someone who is evil but can easily blackmailed with information about how to be involved with that evil military. After the release of the Blacklight Virus, they want to know why Blackwatch's involvement in it's creation so Karen pulls strings with them to get Alex to work with her and hopefully let something slip up. Because of the wire, the FBI finds out about Alex is really the Blacklight Virus and made her sell out Alex as part of a gambit to get him to pin Blackwatch.

The virus causes claustrophobia
Why are so many people outside when they should be at home? Because early virus infection causes them to feel trapped indoors, making them leave their homes to wander about and infect more people. It also causes brain damage as represented by the artificial stupidity.
  • That would mean that a lot of those people are either going to die or become zombies. Maybe the Redlight virus has two strains, the typical turn-or-die zombie propagator spread by direct contact with bodily fluids or zombies, and a weaker but much more contagious airborne strain. The only symptoms of the weaker strain would be headaches/migraines, a preference for the outdoors, perhaps the occasional cough or sneeze, delayed reflexes and easily being confused. None of those alone are anything to really watch out for and are probably going to happen in times of prolonged stress (like a zombie apocalypse while trapped on an island), meaning the civilian has no idea they're infected. Easy prey for the Infected and for turning into Infected, particularly if the weaker strain makes the civilian more susceptible to the strong zombie-making strain.

Cross is somehow related to Batman
They're both extremely powerful but not superpowered individuals, who use high tech equipment and their wits to destroy their enemies. If he isn't a blood relative, I think cross was trained by Batman.

The Alex Mercer who injected Heller isn't our (anti) hero...
...but Pariah himself, taking the form of Alex Mercer for his own convenience, possibly to turn Heller into something similar to Mercerlight, so he can do...whatever Blacklight is afraid Pariah was going to do by coming into contact with Mercerlight.

Alternately, Alex had split off the part of his gestalt personality that remained from the original Alex Mercer. He tried to kill it via dumping it in the ocean, but it didn't stay dead. This separate Alex is the one fought in Prototype 2.

PARIAH becomes The Ancient Enemy
Maybe PARIAH evolves in this in a near future...

Somewhere inside Alex there is a pile of radios he ate along with their owners but couldn't digest.
He uses them one by one to get that military radio feed and spits them out once the battery is drained.

Heller is actually Alex's good side.
Because the next DLC promises a Mercer skin.

Prototype 2 isn't canon
It seems more like a tie-in or Alternate-Universe story than a sequel, as the feel to it is extremely different from that of the original, and the Virus has been claimed only to take female runners, only making an exception for Alex and PARIAH, so they obviously dropped a lot of details. Otherwise, Heller's just a Mary-Sue in a convoluted fanfiction.
  • Magic of retcons, my friend. New canon overwrites old canon to fit.


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