Alex went through Blacklight puberty.
So by the time we see Elizabeth Greene for the first time, she's been infected for about, eh, 40 or 50 years, depending on when Prototype 1 takes place. We have no idea what she was like for the first few years. (There is a Web of Intrigue node that talks about Greene staying in one place for a very long time and not decaying, which might debunk this theory if it mentions the specific amount of time she's been sitting there — I cannot recall the exact figure.) She might have maintained her own personality for the first few years, then... then the urge to reproduce started to emerge, like a human going through puberty. What if the same thing happened to Alex? What if the Black/Redlight life cycle involves amassing as much organic material as possible over the course of a year, then spending it all on spreading itself extremely quickly? If Alex had survived for a few more years, I bet he'd have developed pale, blotchy skin and a Voice of the Legion. And the same thing will happen to Heller, too...

Alex was influenced by all the assholes he had consumed.
Think about it, the Blacklight Mercer became an anti-heroic savior who was willing to die to save the city. However, he's also got the brains of thousands of the most evil people on Earth up in his brainpan. Perhaps, unconsciously, having that many psychopaths and sociopaths influenced his apathy and eventual hate for humanity. Basically, it's like schizophrenia, but with the voices numbering in the thousands and all of them saying pretty much the same thing.

The crow Alex consumed from the previous game will be a Chekhov's Gunman.
We all know that Prototypes are capable of consuming biomass, skills and memories of others; for god sakes, they can even disguise as them, so it shouldn't be surprise to actually have an ability belonging to an animal, such as flight.
  • Not quite; although Mercer never exhibits bird like flight, there is a new enemy type indigenous to the Red Zone which is essentially a giant red bird. It is in fact the only enemy type with a clear animal inspiration among the infected.
  • One of Mercer's powers in the Final Battle is sending a swarm of the infected birds at you. Maybe related, maybe not.

James Heller and Alex Mercer are one and the same person.
Think about it.
  • Jossed

Heller's call-sign will be "Prometheus"
Prometheus stole fire from the king of the god's, Zeus. Alex's call-sign in the first game was Zeus. Heller got his power's from being infected with Alex's Blacklight virus- metaphorically stealing his fire. Therefore, his codename is Prometheus in the interests of thematic consistency.
  • Not sure about this, since a proper military operation would want to give it a name that is both distinctive and easy to say. 'Prometheus' is a bit of a mouthful when there's explosions going off all around and you're shooting at a nigh-unstoppable killing machine that wants to punch your limbs off. 'Ares' would be just as fitting (Heller is a soldier after all) while being quick to say over a radio, and it keeps with the Greek god theme too.
  • In my opinion, Hercules would be a better name; in Greek Mythology, Hercules was a noble warrior who too lost his wife and kid(s). Given birth by Zeus, he was hated by Hera and was then forced to kill his own family—Heller lost his own family, developed deep hatred on Alex (whom is called "Zeus"), and got powers in return. Not very accurate, I know; and second, Heller never stole anything from Alex, on the contrary, Mercer gave him those powers.
  • Jossed. The Most Heller gets called by Blackwatch is "Tango Primary."
James will unknowingly be manipulated by Alex and Blackwatch.
Alex would gain James' upgrades, tendrils, and biobomb powers if he absorbs him.
Just how obviously powerful he has become. Unlike in the first game, where Alex only unlocks his powers and doesn't get any powerful, James would not only unlock his powers, but also would get upgrades.

Alex is not present by the moment James almost died fighting against the infection.
Alex planned on having James set up the fights in the Red Zone, so unless it is confirmed that he did infect him for a reason, he is not present in the moment where James is almost crushed by a falling debris of a building.
  • Jossed in two ways. First, he doesn't almost die that way (it's a car crash). Second, Mercer is not only there, but leads Heller around, watching and testing him silently with various obstacles.

Alex infected James so that he could be his Legacy Character.
The truth is he can't just take down Blackwatch by himself as they would grow more and more powerful alert of him if the infection keeps up on spreading.

Alex's plot of spreading Blacklight beyond NYZ is perfect to take down Blackwatch.
For my opinion, it's obvious that Blackwatch would stop fighting if the infection is stopped.

Death is responsible for Heller's near-death experience.
Oh, I don't know. A survivor of Flight 180 or Route 23 maybe? It would seem he can't kill him by the virus monsters; all his entire life, he cheated Death, even from a war at overseas. He then uses Heller's fight to cause his death. Of course, Alex has foiled it by infecting him. Due to the fact that Heller has become a monster that could never die, he is removed from Death's list.

Mercer created Heller to help him level grind.
Let's say Mercer wants to be stronger than he already is, possibly to escape NY, bring down Blackwatch or a similar major task. But his drive is gone. He's fulfilled his main goal, he's got his revenge and now he's just not determined enough to do it all by himself.

Enter James Heller.

Suddenly, there's another viral megamutant out there, with insane destructive powers and a thirst for revenge. And when Heller's been a wanted mutant for a couple of weeks, it might only take a good Hannibal Lecture to bring him over onto Alex's side.

Alternatively, one will consume the other, massively increasing the other's power. No matter what happens, there's at least one megamutant left with the power to do whatever Alex was planning.

  • Welcome to the top of the food chain.

Greene is still alive.
Basically, the thing Alex consumed was a duplicate created by Greene. She was capable of coherent speech and some complex planning, she'd have a bit more in her head than just random haze like the other infected.

She could have even been hiding inside another part of her One-Winged Angel, waiting for Alex to nom the duplicate before crawling back into the sewers and going dormant. Redlight is patient remember, she might just sit there until Blackwatch is gone and the city is completely clean before spreading The Virus again.

  • Jossed. Mercer fills her role.

Dana Mercer's role.
According to Ken Rosman, she is set to appear for Prototype 2. Here are the suggestions of her role:
  • Alex's mission giver.
  • PARTLY CONFIRMED: She's in it, and she's woken up from her coma. However, her whereabouts are unknown and we don't know her role just yet.
    • Dana works against Mercer by providing insider intel to Father Guerra and Heller. She has renounced her brother and no longer considers him the man she once knew.

The reason Mercer infected Heller is...
  • To spread the infection beyond New York Zero.
  • Make him a bigger threat than him.

The reason Barry Pepper doesn't reprise as the voice of Alex Mercer in Prototype 2 is...
  • His role is only short: Jossed.
  • Busy with other roles to play.
  • Doesn't have enough money.
  • Hates seeing that his character has become a Rogue Protagonist.

Karen Parker's fate.
Ken Rosman also planned on stating of her fate. The most likely fate for her is that she survived against Alex because he doesn't get a Web of Intrigue information from her and doesn't took on her form.
  • Well, her fate has been revealed: she died at Alex's hands/claws/tendrils/whatever. Damn.

Alex Mercer boss fight theories.
Since that it is stated that he is the Big Bad of this game, here are some theories of how the boss fight will come to be.
  • Final Boss.
  • Secret Test of Character.
    • Alex infected James to see if he is a perfect candidate of using the powers of the virus. He berates him of how he complains of wanting to die. This explains of how he is going to make him suffer more. Once James defeats him, Alex will help him in stopping the virus.
      • Jossed.
  • Alex is a Death Seeker.
    • Jossed.

Heller never wanted to die.

Blackwatch plans on having Heller die.
It's because they resent the fact that he survives longer than them against the Blacklight Virus. While in a suicide mission, one of the tanks fire a building, causing the big piece of it to come crashing onto Heller.
  • Why not just shoot Heller? It's not like they really care about friendly-fire.

Heller is going to consume Dana Mercer and Dr. Ragland
Alex spent most of the first game hunting down and consuming anybody who might have even the slightest bit of information on Mc Mullen. Heller is going to be looking on information on Mercer. It makes sense that they'd be Web of Intrigue targets.
  • Jossed

Alex Mercer will die for real in Prototype 2.
According to the Blackwatch trailer, the briefing states that they thought he died from the Blacklight Virus, but they're wrong. It is assumed he is destroyed from placing the nuke to the river, but they're wrong. With another Blacklight being around thanks to Alex, maybe he'll die this time.
  • Confirmed.

There will be a Bittersweet Ending.
I know Activision and Radical Entertainment almost always make games with happy endings, but for Prototype 2, the ending would happy but with sad elements. Here are the suggestions:
  • James will discover Alex is not the Big Bad, but still holds resentment on him for the death of his wife and child.
  • They will team against PARIAH or some other main antagonist, but aren't powerful enough to defeat him.
  • They defeat the true antagonist and save New York City, but at the cost of their lives.
    • Jossed on all counts.

Alex Mercer is still alive.
I'm talking about the real Alex Mercer, the one who created the Blacklight Virus and unleashed it out of pure spite. I know this sounds crazy, but have you noticed the thing about Heller being infected with the Blacklight Virus instead of dying from it? It has the ability to resurrect the dead, although for Heller's case, he's almost in death.

Let me preface this and say that there is no second living Alex Mercer. Major spoilers for [PROTOTYPE 2] note 

The Big Bad of Prototype 2 will be a new top official of Blackwatch.
What he's planning for Alex and James is that he uses the former's research to produce more of the monsters and is really more brutal than General Randall.
  • Jossed. The new leader of the Blackwatch forces in NYZ ends up helping Heller in the end, while Alex is the Big Bad.

Alex Mercer infected Heller to create a dragon.
Alex created the red zone as a test. The goal: find the toughest man in the military/Blackwatch to infect. This man is given Alex's powers at a low level and forced to evolve by fighting other infected so he will know both what the infected are capable of and what their weaknesses are. The reason this isn't being done in an arena setting: this isn't merely a bodyguard or a faster way for Alex to grow stronger. Heller is going to be his general. Additionally, at the end of the game, Alex will offer Heller his family back, and the player will have a choice: join Alex, or consume him.
  • Semi-confirmed, but not to the degree specified above.

James Heller never existed.
It's all a dying dream by Alex who actually died in the explosion of a nuke. He just dreamed of stopping the virus.
  • Jossed.

Alex Mercer created Heller so that Heller could kill him.
It seems to me that Alex started to gain something resembling a conscious by the end of the game. Now, we don't know when Heller came back to find his wife and daughter dead. It could have been during the game, in the middle of Alex's rather lengthy rampage phase. I think Mercer is feeling the weight of his new conscious and all those memories and has decided the world is better off without him. Problem: short of finding another nuke for the military to throw at him, nothing seems capable of doing that. So what does he do? Find a man of moral fiber (well, more moral that Mercer was) and a good honest-to-god reason the loathe him utterly., inject him with an upgraded version version of Blacklight, leave him alone for a while to gain power, and boom. Suicide By Eldritch Abomination.
  • Jossed.

The Alex Mercer in Prototype 2 is the real Alex Mercer.
In the original Prototype the protagonist was really the Blacklight virus made sentinent. The true Alex Mercer was a ruthless bastard that caused the infection out of spite. So lets say that Blackwatch developed a weapon to kill Alex and instead wiped out the mind and personality of the Blacklight virus, the one with the ability to actually have guilt and doubt. In the rebooted version is the original Alex Mercer, the narcissistic sociopath now let loose upon New York.
  • Seconding this ([[Tropers/Speedball]]). It makes perfect sense. The real Mercer was a right bastard.
  • Unfortunately Jossed.

Alex Mercer has taken control of the virus to protect Dana.
Dana could be infected or still comatose, either way Alex is going to want to protect her. So he takes over the infected, builds this massive hive thing in the middle of other hive things, stocks it full of guard zombies, and sticks Dana in the middle to keep her safe. If she's infected, he controls her so she stays there and doesn't die. If she's comatose, he keeps her there so she'll be protected when she wakes. His control keeps the infected from eating her. He only does this because he either has hope she'll wake up normal (if comatose) or because he can't bring himself to kill what he considers his own sister (if zombified).
  • Jossed. She denies he is even her brother anymore.

Alex is having a three way split personality fight between Blacklight Alex, Elizabeth Green, and Supreme Hunter Cross
By the end of the first game he had killed two other Blacklight infected humans that had similar abilities to himself. It could be possible that Blacklight Alex is becoming insane after doing so and is losing control of his mind to Elizabeth or Cross who were planning to infect the whole world with the virus. He could have infected Heller to put an end to himself before he did something he could regret, and He couldn't just get gunned down by any random mook because of the chance that Blackwatch would take his corpse in and start the mess all over again by using his body as research.
  • Jossed.

Alex is the one who secretly gives Heller his missions.
Unlike him, who gets his missions from person to person, Heller gets his missions at the Blackwatch computer. How did he get all this information from this device? Here's the thing: Alex secretly hacked into it and gives information of the virus to be fought.
  • Jossed. While he does give one mission, it's never a secret.

Alex infected Heller so he could kill Dana
Dana will have turned out to have been infected when she was kidnapped in the first game. Now she'll take over Greene's posistion as hive queen. Mercer can't bring himself to kill her. So he makes someone who can- Heller.
  • Jossed. He didn't want to kill her.

There is more than one Alex Mercer out there
Okay we say at the end of the first game that Mercer can regenerate from even a tiny scrap of flesh. But maybe multiple scraps regenerated. In this way Radical could do an evil Mercer, and still be able to bring him back for later games.
  • Possible, but these "other" Alexes must've left New York before their counterpart started the second outbreak; Otherwise, they would've noticed their counterpart's actions and tried to interfere (or join him).
    • Or were eaten by him.
  • To expand on this one, Alex was torn into at least two scraps. One, which possessed more of the original Alex Mercer in him, was the one involved in Prototype 2. Another, much closer to the Alex Mercer at the end of Prototype, kept a lower profile because he knew that the one involved in the main plot of the sequel would destroy all of NYZ to get to him. Plus, once Heller became involved, exposing himself would result in Heller going after them both, while hiding would take care of the other Mercer without making himself a target.
    • I really like this. I hope this is how things turn out if another developer picks up the series.

Heller will come back as a disinterested third party for the next game.
He's got a reason to not go the same path as Mercer did (his daughter's still alive) so he'll probably try to keep a low profile, tending to his own business and whatnot. Perhaps a plot point will involve him getting forced out of retirement in order to protect his interests.
  • Of course, for a third game to happen, wouldn't it be necessary for Heller to infect someone to be the new protagonist?
    • Not if the theories involving multiple "copies" of Alex are true. There's also one other runner who's remained in the background so far: Pariah.
    • Not necessarily. In a blink and you'll miss it moment in a cutscene before a red zone mission to grab a government agent, we see that Heller's daughter is code named PARIAH.

Heller will be the villain of the third game.
Just to establish a continuing Running Gag for the series.

The influence of Elizabeth Greene inside Alex Mercer is what contributed to Mercer's similar Hive-Mind spreading tendencies.
Elizabeth Greene wanted to spread the Redlight lifeform under her control. After eating her and getting disappointed past a point of no return, Mercer wants to spread the Blacklight lifeform under his control. All with a similar topping-the-food-chain pretext.
  • And now that Heller has both Greene and Mercer inside his being, who knows what'll happen next?

The Alex Mercer in this game is not the Player Character from the first game
It had to be said. Besides, a few things are left suspiciously vague, such as why he infected Heller. There was no way Heller could further Mercer's plan by having him infected. And why is there a video with him in the center of the shot, in his Shapeshifter Default Form, releasing the virus at Penn Station?
  • It is entirely possible that after the nuke went off in the first game, different pieces of Mercer washed up in different parts of the city, and grew into separate entities.
    • The original human "bad Mercer" may have been locked away, so to speak, inside virus Mercer throughout the first game, just barely alive, and the nuke separated that piece from the rest of the virus' body and allowed "bad Mercer" to regain consciousness. The evil part may have not been aware that he was locked away in the first placed and gained memories of the first game's events. Meanwhile, the rest of Mercer may have been mostly incinerated, with the few surviving parts regenerating into new Mercers, but severely weakened. These good clones may have had to find each other and re merge while avoiding the bad Mercer. The Mercer in the midquel comics could have been a completely different entity than these other two. Alternatively, bad Mercer may have consumed good Mercer, and good Mercer influenced bad Mercer to make Heller an Evolved. That would explain some of the faulty logic in Mercer creating someone who could defeat him.

'Heller' is a Meaningful Name
Following a similar line of thought as the MRSA = Mercer theory, the name 'Heller' sounds an awful lot like 'He La', an immortal cell line used in scientific research which because of horizontal gene transfer is essentially a hybrid between human cells and a virus. It's also known for being difficult to control and having a tendency to contaminate things.

Alex Mercer consumed Albert Wesker between games
You've gotta admit it explains a lot.

Alex Mercer being the villain will be Retconned or be subjected to an Author's Saving Throw.
The negative reception to the ending will make it so that they're going to end up ignoring all the tie-in novels and other things that explain Mercer's change in character and try out an alternate explanation.

The more heroic Alex Mercer most people identify as in the first game does exist.
In the form of the Alex Mercer skin for Heller. Which sort of a sister theory to the ones about Alex clones. Either that, or Heller activates the skin after consuming Alex and thus completing story mode as a sort of trophy. Or something.

The Evolved in Gentek and Blackwatch are responsible for the lower number of virus detectors in this game.
In the original game, the D-Codes and UAVs both could detect the virus, and by endgame all military bases had multiple overlapping detectors, making it hard to get inside a base without setting off the alarms at least once. Yet in 2, the Orions can't tell who is infected, and the UAVs don't have one on board either. Also, despite the fact virus detectors cannot be sabotaged, there usually aren't enough to provide as much coverage as the detectors in 1. Since the Evolved were infiltrating Blackwatch and Gentek, it would be in their interests to try and keep the amount of things that could detect the virus as low as possible.

There will be a legit Five-Man Band in Prototype 3 (if it comes out)
To list things up: Mercer was pretty much on his own, Heller had only 2 allies with him at the end (3 if you count Rooks as a potential ally), so why not an actual team in the sequel? By my estimate, the following will go as this

Alex survived the final battle thanks to Ragland, who was purposefully remaining concealed as part of a back-up plan.
Ragland is a doctor who helped Mercer in the past, knows a great deal about the various viruses, and already helped Alex heal from one crippling injury. As such, if there was one person by this point who could be trusted to ensure Mercer survived his final battle with Heller, with Dana having switched sides and his Evolved being used for a quick power-up, it would be him. So, Ragland would have needed only a small amount of Biomass, and with Heller tearing off arms all over the place he would have easily been able to find it. Since Alex was able to reform himself from a crow, it shouldn't take too long for him to get back on his feet, start licking his wounds, and possibly preparing for round two.
  • Why would Ragland even do that? He worked with Mercer mainly out of fear and guilt. I can't see him willingly aid and abet Mercer if Alex was trying to more or less destroy humanity, so what reason would he have for trying to resurrect Alex?
    • Becoming Evolved?

Mercer infected Heller to help him stop a bigger enemy. Pariah.
Including the consuming part. Regardless of who consumed who, Alex knew that the victor would stand a better chance of fighting Pariah.
  • Then wouldn't this be something Heller would have immediately discovered afterwards?

"Mercer" was actually Supreme Hunter who survived the first game.
We saw the thing recover from being completely liquefied. It's clear that "mere" decapitation couldn't do more harm. It was never caught in the nuclear blast and instead was left out of sight - long enough to recover and escape. It then went into hiding, consuming people here and there by one, and then grew strong enough to either catch and consume Mercer, or become able to take his shape and powers basing on part on DNA it inherited from him. With the original dead or gone from NY in search of Pariah, Supreme Hunter took his likelihood in order to frame him (and be of more humanoid shape to cooperate with people easier) and started the mess again. This kinda explains "Supreme Mercer"'s new traits such as the ability to infect people, spread the virus directly from his mass and control all infected (inherited from Greene), strategical scheming (inherited from Cross, whose manipulations in the first game came close to Xanatos Gambit), totally egoistical, megalomaniac personality (its own contribution) and the fact that all infection suddenly started glowing like molten metal (Redlight, get it?).
  • While I'd prefer that to what we actually got (though it'd be hilariously anticlimatic if the protagonist of the first game died offscreen with absolutely no mention), the prequel comics pretty clearly show that it is Alex. Though I guess you could disregard them...

Mercer's form may have been the one Heller fights, but he isn't doing this of his own free will.
The Anchor is broad strokes canon. In-between the two games, Alex and Ragland travelled across the world not just for Alex to better connect with humanity, but to get rid of any remaining traces of Blacklight, and ensure nothing like Greene happens again. During this time, Alex ends up confronting PARIAH... and just beats and consumes him. In fact, he does it TOO easily. In truth, after Alex consumes him, PARIAH procedes to suppress Alex's personality and kills and consumes Ragland to drive Mercer over the Despair Event Horizon. Alex only maintains enough willpower to make sure PARIAH doesn't hurt Dana, while the son of Greene uses his form as a scapegoat for the NYZ infection. Cue Heller, who PARIAH merely sees as a potential Evolved, but who Alex ends up seeing as his shot at stopping PARIAH, even if he, himself, must die. Note: This Troper has only played the first game, and got the info for all other material from here and Youtube.
  • Pariah's pretty much dropped out of the plot; he was never mentioned in the Web of Intrigue in P2, nor was he mentioned in the prequel comics, where Alex was walking the Earth. So it's rather unlikely.
  • As revealed in a blink and you'll miss it moment, Heller's daughter is code named PARIAH by the government agency that holds her. Whether or not this is the same PARIAH is anyone's guess.

Everything went exactly as Alex planned...
What's the first thing Heller does after he consumes Alex? He unleashes a Devastator attack so massive that it spans throughout all of Manhattan and, possibly, all of NYZ. Effectively wiping out the Redlight virus. To do something like that, Heller would need a massive amount of bio-mass. Like say, the collective bio-mass of an entire army of evolved that Mercer just happened to absorb before his final fight with Heller thus giving Heller one big juicy meal to chow down on. Not to mention all the other Evolved Mercer sent after Heller or lured Heller to despite the fact that Heller was clearly more powerful than any of Mercer's army. And having sleeper agents in Blackwatch doing all of those experiments? Those projects he had his agents do either helped Heller become more powerful in some way or lured Heller to massive Blackwatch projects that, once Heller went all apesh*t on them, would have severely hurt Blackwatch. In the end, Mercer needed Heller to be the one to gain all the bio-mass both of them, as well as the evolved, accumulated over the course of the past two games because Heller had, and I quote, "Resilient DNA". That whole plan to march on humanity with an army of Evolved? Kinda hard to do that when you just ATE your army. And having Heller's daughter become 'the queen of the new world'? Just a way to lure Heller to their final battle. A way to make Heller hate him. Alex wanted Heller to hate him... because he wanted Heller to kill him.
  • WHY? To be honest, if all of what Alex did was a ludicrously circuitous suicide attempt, I'd argue that's actually worse than him being a generic evil overlord. Because the virus was being wiped out UNTIL ALEX UNLEASHED IT AGAIN. He killed a city of millions, a city he risked his life to save, because he didn't want to live anymore? Why not pitch himself into a volcano? Or consult a psychiatrist? Or do anything that doesn't involve genocidally unleashing a death plague on Manhattan AGAIN. I mean, him being an incompetent villain is one thing; not optimal, but I get it. It being all a plan to kill himself makes him both look incredibly dumb, and possibly even eviller, because all those people he killed weren't casualties in the path of him creating a perfect world, but he killed them essentially to piss someone else off to kill him. Plus, it contradicts the ending to the Anchor; he's not despondent or anything, his motivation is disdain for humanity. Trust me, I'm all for coming up with a reason to explain away his characterization, but it all being a suicide attempt irks me.
  • I meant that Alex needed Heller to gain all the Bio-mass because he was the one with the 'resilient DNA'. I wasn't saying Alex was suicidal or that he wanted to die but rather he felt he had to die so that the virus would finally be wiped out. But, yeah, the fact that Alex unleashed the virus a second time kinda debunks my theory doesn't it? Man, I don't WANT Alex to be a crappy Bond-villain.
    • Sorry I misread your post.
  • Maybe... he didn't? There's no real indication that the virus was dying after Greene died. And the original poster did say Alex wanted Heller to hate him. Maybe it wasn't the virus Alex unleashed but just some red gas. I fake virus that would make Heller blame Alex for his families death more than he already had and thus make him hate Alex even more.
    • In the scene where they watch the footage, Guerra notes that Athena's contacts had examined every possible means of infection, and that the second outbreak did start at Penn Station, the day Alex did the weird virusy thing.
  • Blackwatch was doing more bioweapons research on blacklight right? Well, perhaps they were ready to release their own verion on the public, one which couldn't be controled, so to stop them Alex starts the second outbreak, filling Manhatten with a blacklight version HE controled. But he now has to stay there most of the time to control it, only being able to take short trips to the yellow zone, so to keep spying on blackwatch he creates the evolved, and through them in time he realizes unless something is done blackwatch will become unstoppable, the evolved are not capable enough, he needs another him. Que Heller, a survivor with nothing to live for outside of a need to kill those responsable, Mercer makes Heller into a new prototype, using all sorts of new upgrades and potentials he cooked up over time, and sets him loose on blackwatch. After seeing Heller in action, he knows that Heller would do the right thing, so he acts the villian to persuade Heller to kill him, thus ending the threat of Blacklight forever. Unfortunatly, being a mix of a sociopath who probably never saw a good movie in his life, a virus factory who has been out of the world sinces the 60's and the b-movie era, and Cross, who lets face it didn't seem like a guy who did normal things for fun, all the experience he has with "villians" will be cheesy b-movie villians and possibly ones from like saturday morning cartoons, who are not much better, and in many cases way way more hammy. Thus, with b-movie plots to back him up, he decides to become the "take over the world with my evil army" villian, which turns out as we all know.

Both Blacklight and Redlight were created using information collected from a Marker...
And Greene, Mercer, and Heller were the makings of a Brethren Moon. I mean look at the viral biomass and compare it to the biomass left behind by a Necromorph outbreak. They are very similar in appearance, to say nothing of Mercer's plan...

Part of Alex wanted to die.
Just hear me out on this one. During the final battle, amongst his constant taunts, Alex is also giving you advice on how to beat him, hinting at which powers to use and how to avoid his attacks. Not to mention "Welcome to the top of the food chain."

Mercer isn't completely dead.
After consuming so many people and infected, he learned how to preserve consciousness in the event that he gets consumed and take control from within. If there's a next game, Alex will resurface through Heller a la Grand Theft Me.