Dr. Alexander J. Mercer/ZEUS
Voiced by: Barry Pepper (Prototype 1), Darryl Kurylo (Prototype 2)
The protagonist, a man who wakes up in the GENTEK morgue with bizarre and horrifying powers and no knowledge of events prior to that point, aside from his name and that he was once a scientist. Confused, enraged, and determined to reclaim his past, he sets out to do so by hunting down his old colleagues.
- Absurdly Sharp Claws: The first power Alex gained were four-fingered two-foot long talons.
- Aloof Big Brother: The real Alex only cared about Dana as a tool for his purposes. However, after Heller consumes Alex at the end of Prototype 2 and absorbs his memories, Dana can be heard remarking that they used to play games, skate, and watch scary movies together. So, apparently he wasn't always like this.
- Amnesiac Dissonance: No matter how much of a monster you play Alex as, the man whose form he took was worse.
- And Then John Was a Zombie: One of the most horrifying examples ever put into a game or comic. You thought the Alex Mercer you knew and played as is merely a superpowered Zombie Infectee? No, he is The Virus!
- Anti-Hero: Initially a straight-up Villain Protagonist, but becomes this status by the end of the first game due to Character Development. Whether he's a Nominal Hero or an Unscrupulous Hero depends on the actions of the player.
- Ax-Crazy: it doesn't depend on whether or not you go after civilians, because either way, your target is going to be subjected to a lot of homicidal fury which usually ends in the victim killed gruesomely or being lunch.
- Badass Bookworm: In addition to being a former scientist, he absorbs the knowledge of anyone he consumes, and he'll consume upwards of thirty scientists completing the Web of Intrigue - though he doesn't exercise it much.
- Becoming the Mask: Played with. The real Alex died; the player character is just The Virus using him as a mask. But the virus has some redeeming qualities and is fiercely protective of Dana.
- Berserk Button: Lots of things, but especially don't hurt his sister or throw innocent people into his path to save yourself.
- Big Eater: Soldiers, civilians, infected, Hunters; he can and will absorb thousands of them alive (and in the humans' case, whole) throughout the game. One of the Achievements is even called Endless Hunger.
- Blade Below the Shoulder: The Blade power, more like the "replacing your arm with a blade" variant.
- Blood Knight: He actually seems excited at the prospect of fighting a whole pack of car-sized flesh monsters. The player will likely disagree.
- Body Surf: In his own way, it's entirely possible to go undetected in a military base or during a mission by stealthily consuming and stealing the identities of one soldier after another. This has nothing to do with the explicitly named "Body Surf" power.
- Brought Down to Badass: Downplayed. At one point in the game he's infected with an artificial parasite that feeds on him and negates his ability to create Shapeshifter Weapons. Alex still retains his Super Strength, Super Speed, Disguise power, and Healing Factor, however.
- Civvie Spandex: When not armored up he wears a shirt, hoodie, and jacket, jeans, and shoes.
- Combat Pragmatist: Fighting fair is hard when you can kill a person with one negligent gesture, so he doesn't bother holding back his Super Strength in serious combat.
- Combat Tentacles: The Whipfist, Tendril Barrage, and Critical Pain Devastators.
- Creepy Blue Eyes: His main distinguishing features are his unusually pale, creepy, reflective eyes.
- Cursed with Awesome: All these incredible superhuman abilities? He believes they (along with his amnesia) were a side-effect of being afflicted with the virus when it was unleashed and wants them "cured".
- Dead All Along: The shapeshifter tearing up Manhattan searching for his memories is just the sentient Blacklight virus wearing Alex Mercer's corpse.
- Dead Person Impersonation: Courtesy of eating them and taking their form. An unintentional example of the virus taking the real, deceased Mercer's form.
- Determinator: The Blackwatch only ever manage to slow him down, even once he becomes their biggest threat and they throw everything they've got at him.
- Driven to Villainy: Nobody ever asked him whether he wanted the powers he has, or whether he wanted to be treated like a monster. That he acts like one is in some sense a function of his circumstances, at least at first. The trope is ultimately played straight, subverted, and inverted.
- Eerie Pale-Skinned Brunette: The only colors in his face are the red circles under his eyes; even his lips are pale. He looks like he last slept when he was dead.
- The Empath: In a very messed up way, he absorbs so many people that their screaming in his head forces him to develop a conscience. He is extremely unhappy about that.
- Even Evil Has Standards: As ruthless and violent as ZEUS is, even he was disgusted when he learned what his creator did.
- Evilutionary Biologist: The real Alex Mercer fits this to a T.
- Extreme Mêlée Revenge: The default animation for consuming a Web of Intrigue Target sees Alex knock his victim to the ground, pin them, and then just punch them viciously, over and over until their faces cave in. It's so brutal it even sprays blood on the camera.
- Face Stealer: The basis of his "consume and become" abilities, along with Brain Food.
- Four Eyes, Zero Soul: The real Alex sported glasses prior to his death; the virus doesn't need them.
- Freudian Excuse: In his character profile (and hinted at very obliquely in the game) is the story of Alex Mercer's horrible, poverty-stricken childhood being shipped around foster homes until his mother was released from jail. He would have preferred the foster homes, and eventually made his escape through his gift for science, viewing the high-profile job and excellent paycheck he received at GENTEK as owed to him by the world after his crappy life. When he learned that Blackwatch was going to purge the project, that was the final straw.
- From a Single Cell: Even after getting nuked, all he needs is a few scraps of his body and some biological matter and he's back in business.
- From Nobody to Nightmare: He went from plain troubled kid to scrawny scientist to Humanoid Abomination able to fight the undead and the entirety of the U.S. Army simultaneously. But the original turned out to be much worse than the viral abomination that replaced him.
- Hates Being Touched: Quite minor, and for one scene, but Alex's reaction to Karen's welcoming embrace is to freeze uncomfortably and then shrug her off. Understandably, nobody else ever even tries to approach him with affection and he never approaches anyone likewise — except once, with Dana, trying to comfort her.
- Hijacking Cthulhu: Is a viral abomination, but retains his human consciousness.
- Hurting Hero: He's clearly hurt by Dana's reaction upon seeing him killing a Blackwatch soldier, and then again to a greater (but more subtle) extent when he confesses that he can hear the voices of the people he's killed inside himself but believes that killing "feels right". He later apologises and she tentatively accepts him again right before a Leader Hunter bursts through her wall and kidnaps her.
- Identity Absorption: His baseline and most useful ability, though it's not without side effects such as developing a conscience.
- I'm a Humanitarian: He gains health, knowledge, powers, skills, disguises, and pieces of the Jigsaw Puzzle Plot by absorbing people.
- Immune to Bullets: Functionally if not completely. Alex doesn't even flinch when taking gunfire, as if the bullets are merely passing through his biomass without doing any harm. Unless you're playing on Hard, it takes a lot of massed gunfire to even come close to seriously damaging him. In cutscenes, he's able to get up from being shot by five guys armed with assault rifles.
- Instant Armor: The Armor power grows hardened biomass that covers the entirety of Alex's body.
- In the Hood: He wears a hood for much of the game in his default form, and while his strength and speed are frightening it's his shapeshifting and stealth abilities that make him so dangerous to Blackwatch.
- Jerkass: Selfish, vicious, violent, devoid of tact, almost hilariously bad at showing or receiving affection, and either borders on or is actively sadistic depending on the player. The original Mercer went beyond "just" being a jerk, but his influence is likely at work.
- Jerk with a Heart of Gold: Later, due to Character Development.
- Kill and Replace: Or "Consume And Become", as he phrases it. No difference in context of the trope.
- Knight Templar Big Brother: Mess with Dana and you better have a way out of Manhattan, because no place on the island is safe. You're not even guaranteed safety if you escape.
- Lack of Empathy: The original Mercer did not believe morality was a part of his job, and had no problem altering an already dangerous bioweapon to become even more dangerous.
- Lightning Bruiser: The only thing in the game that can keep up with him is an attack helicopter, which he can kill in two hits. On the Infected side of things, Hunters and Leader Hunters are technically faster, but suffer in maneuverability compared to his speed.
- Lovecraftian Superpower: Strong enough to casually rip humans apart with his bare hands? Check. Produces a black and red, fleshy substance from his body that can be molded into various weapons? Check. Heals himself by absorbing people's flesh into his own? Check.
- Luckily, My Shield Will Protect Me: The Shield power. Although breakable, it regenerates after a few seconds on his back.
- Mad Scientist: The real Dr. Alex Mercer, at your service.
- Mind Hive: He keeps every one of his consumed victims' memories inside his head, and he says he can still hear them all screaming as he relives their deaths over and over and over.Because everyone I've killed... They're in me. They are me.
- Monstrous Humanoid: After The Reveal, it is revealed that he is a human-shaped pile of The Virus that took the original Mercer's memories, name and form. You've been playing as The Virus all along, with it thinking that he was Mercer. However, even after this revelation, he still wears Mercer's form and remains protective of Dana despite him not really being her brother.
- Morally Ambiguous Doctorate: The certificate is on the wall of his apartment. And boy was he evil. Good thing we don't play as the guy who earned the doctorate.
- Muscles Are Meaningful:
- The Musclemass power bulks up his arms with hardened biomass and they do enhance his Super Strength while engaging in basic hand-to-hand combat or throwing objects around.
- The Hammerfist power turns this Up to Eleven by enlarging his arms enough that they become heavier than the rest of his body, granting the capability to trash vehicles with ease.
- Muscles Are Meaningless: That being said in Muscles Are Meaningful, he actually looks pretty gaunt and scrawny most of the time outside of the Musclemass/Hammerfist powers. That doesn't stop him from throwing cars around, knocking out helicopters with a single kick, and punching through steel doors two feet thick with ease.
- Oh, Crap!: Seeing the two pathologists who were examining him get executed by Blackwatch, getting his cover blown infiltrating a Blackwatch announcement, and an unexpected Infected attack disrupting his plan to "interrogate" McMullen. Although, being Alex, his version of that last one is a little more M-Rated: "SON OF A BITCH!"
- One-Man Army: Within the city are Blackwatch, a merciless paramilitary organization aided by the U.S. Military, and a virulent, devastating, Zombie Apocalypse causing virus, and both sides rightfully regard Alex Mercer as the single most dangerous thing there.
- Person of Mass Destruction: General Randall sums up his awakening as; "He's eliminated fifty of my men and smashed through a two-foot steel door." Once his powers are fully upgraded, he's capable of single-handedly slaughtering hundreds of men along with multiple tanks and helicopters in minutes.
- Plaguemaster: Considering that he's a sapient strain of the The Virus itself given human form, this is a given. To add to this, he can also spread his plague to others.
- Power Fist: The Hammerfists power enlarges his fists with Super Strength than can tear enemy vehicles.
- Predecessor Villain: It was revealed that the original Alex Mercer created the virus and started the outbreak before his death, leading to the conflict in the game.
- Present Absence: Doctor Alexander Mercer's actions kick off the entire main plot and provide the motivations for at least two major characters, despite him being dead before the opening cutscene.
- Promotion to Parent: According to the backstory, Alex was actually more of a paternal figure to Dana than their actual mother ever was.
- Psychotic Smirk: Alex never really smiles, but he's prone to these from time to time. Specific (and creepy) examples are after he thinks he's beaten Cross and when he gets the drop on McMullen.
- Quest for Identity: His goal is to find out who he was before he lost his memory. Once he finds the truth, he immediately wishes he'd never learned it.
- Roaring Rampage of Revenge: His other goal. The virus is a grotesque sickness afflicting both him and his city, so he wants to track down who released it and make them pay.
- Roof Hopping: Due to a combo of Le Parkour and In a Single Bound. Some optional events enforce this as you go around checkpoints scattered in nearby rooftops.
- Shapeshifting: The entire basis of his powers that don't revolve around eating people.
- Shapeshifter Weapon: He can scavenge guns from Blackwatch and the military, but most of his weapons come from transforming his arms.
- Shockwave Clap: A variation with the Knuckle Shockwave attack; he pounds his fists together rather than clapping his hands.
- Sir Swears-a-Lot: Maybe it's a side-effect of eating all those soldiers.
- The Sociopath: Mercer is diagnosed a narcissist and a sociopath in one Web of Intrigue cutscene and the lack of a Karma Meter - along with the sheer scope for destruction that his powers have and the way they're fueled - means he'll be doing some awful things in the name of his goals. He rarely displays so much as a flicker of regret for the murder, mass-murder, mass-cannibalism, all kinds of destruction, collateral damage... However, subverted in that he does have regrets, even if only Dana and Cross ever see them. That diagnosis was more likely for the original Mercer.
- Spanner in the Works: It turns out that a super-strong shape-shifting man-eating psychopath with an intense hatred for Blackwatch tends to screw up their plans. Funny how that works.
- Spikes of Doom: The Claws' groundspike move, and the Groundspike Graveyard Devastator.
- The Stoic: Alex is normally a fairly calm and subdued person, rarely raising his voice. The few times he does lose his temper, he really loses it.
- Super Senses: Infected vision and Infrared vision.
- Super Strength: Alex at a base level will kill humans in one hit and can lift cars. If you stack Musclemass on top of that, Alex can pitch cars over a city block and gib people in one hit.
- Tranquil Fury: There are moments where the only thing that alerts you to the fact that he's very angry is the venom in his voice. One notable moment where he finally catches up with Karen Parker.Alex: I know.
- Taking You with Me: It's revealed that the original Alex released Blacklight when he was cornered by the Blackwatch. it seems he didn't believe in half-measures - if he was going down, he was taking potentially the entire human race with him.
- Technically Naked Shapeshifter: His clothes are formed from his biomass.
- There Is No Kill Like Overkill: Alex is a guy who believes in being thorough. To the point of coating the ground, walls, and scenery with viscera in his, uh, enthusiasm.
- Tomato in the Mirror: Alex Mercer is hunting down the scientists behind the virus, including whoever caused the Penn Station outbreak. As it turns out, he's The Virus. And the man who designed it and caused the outbreak? Alex Mercer.
- Unstoppable Rage: His ground state of being. He's an angry, angry abomination.
- Unwitting Pawn: Every bad guy manipulates him for their own gain at one point or another. He doesn't like it.
- Villain Protagonist: While his methods are gruesome, it's debatable how much of a villain he actually is — he acts initially in self defense against Blackwatch then pursues revenge rather than causing destruction just for the hell of it. Then again, you are in control of a walking biological weapon willing to devour innocent civilians to preserve his own life, so it goes both ways.
- What Have I Become?: Word for word in his closing narration. His conclusion is that he is "less than human... but also something more."
- Wolverine Claws: The Claws power turns his fingers into blades.
- Wrestler in All of Us: Several of his normal moves. One of the default consume animations is a chokeslam.
- The Virus: The source of his abilities. But not the way you think — "Alex Mercer" is the Blacklight virus taking the memories and form of the deceased scientist Dr. Alex Mercer.
- Woobie, Destroyer of Worlds: You can't help but feel bad for Blacklight-Alex a lot of the time. Surprise! You died. Surprise! You have no memory. Surprise! You unleashed a plague onto Manhattan. Surprise! YOU DID IT TWICE. (Although only the first time was intentional.) Surprise! You're not really you! Surprise! YOU ARE THE VIRUS. Surprise! The original guy was evil! Surprise! You have a conscience now! Surprise! That means you feel like shit about everything! Surprise! Your not-sister's been kidnapped! Surprise! The city's going to be nuked! The guy just can't catch a break. Granted, this is later subverted by that very same conscience, which makes Alex decide that he doesn't want to make all of the people who get in his way die a horrible death because of his Roaring Rampage of Revenge after all. Just certain people.
- Would Hit a Girl: A few Web of Intrigue targets are women, which naturally requires consuming them. There is no alteration to the violence he uses when doing so. When he finally get his hands on Elizabeth Greene, Mercer viciously beats her to death to consume her.
- Younger Than They Look: Alex looks to be in his late twenties and indeed, the original Mercer was 29, but the viral copy is only 18 days old by the end of the game. He is, however, also ageless; he'll never look any older, either. As long as he keeps fed and whole, he could conceivably live forever.
Alex in Prototype 2
In the sequel, Alex is no longer the protagonist and differs a great deal in characterisation, stemming from some bad experiences in between the games recounted in The Anchor. As such, these are the additional tropes that apply to him in Prototype 2. Spoilers ahead.
- A God Am I: Debatable in the sequel in accordance with his plan. He even tells his sister that the viral monsters are "no longer bound by life and death", and his Motive Rant includes a proclamation that he will create a perfect "new world".
- Affably Evil: In the sequel towards Heller. He even tries to recruit him and teaches him how to absorb memories from his consumption targets. Testimony from his Evolved indicates he's genuinely fond of Heller, and he claims he's disappointed in him for disrupting his plans. Even when he makes the decision to kill Heller off, he tries to give him a quick death. It's only when that fails that the claws come out, and he never stops trying to convince Heller to join him.
- All There in the Manual: The comic book story The Anchor explains the reason for his FaceHeel Turn; after stopping the nuke, Alex lost faith in humanity and took to Walking the Earth in the hopes that he could find something to restore said faith. Instead, Alex just kept finding more and more reasons to think that Humans Are Bastards, which culminated in a woman he had become attracted to stealing his money and shooting him point-blank in the face while openly declaring she only cared about herself. It was this that cemented Alex's change from fighting Blacklight to embracing it.
- Bad Boss: Berates and threatens his underlings during Web of Intrigue segments and consumes them all to boost his own powers in time for his fight with Heller.
- Big Bad: He's the guy that kicks off the whole plot and is trying to Take Over the World.
- Big Bad Friend: In the second game, as his sister, Dana, finds out.
- Blue and Orange Morality: His goal borders on it, if not Insane Troll Logic. Heller is... unconvinced by his arguments.
- Cain and Abel: The Cain to Dana's Abel after his FaceHeel Turn.
- Dark Messiah: Has shades, given the reverence most of the Evolved seem to hold him in. Many of them act honestly shocked that Heller is attacking them.
- Deadpan Snarker: His response to Heller's threat during the Final Boss stands out:James: You're gonna tell me [where Maya is], either on your own, or after I skull-fuck you and drain your memories out the hole!
Alex: (chuckles) Scary!
- Despair Event Horizon: The prequel comics reveal the reason for his FaceHeel Turn in [PROTOTYPE 2] is because he lost all faith in humanity.
- Devour the Dragon: Before throwing down with Heller, he consumes all the Evolved present to boost his own power and go One-Winged Angel.
- The Dreaded: Unsurprisingly, given all the chaos he caused and is still causing; at the beginning of the game, Red Crown's response to learning Alex is in the Red Zone is a very justified "Oh, shit!", followed by them ordering Heller not to engage; Heller doesn't listen.
- Expy: In the sequel, the similarities to long-standing Resident Evil villain Albert Wesker (particularly his characterization in Resident Evil 5) are too numerous to ignore. Both are intellectual, with scientific backgrounds (though Mercer's are borrowed), who started an endemic with a weaponized virus, who wish to wipe the scourge of humanity with a bioweapon of mass destruction, are extremely dangerous warriors augmented with the same virus they plan to use to wipe out the planet, and all of the aforementioned viruses result in veiny, bulbous, tendrily, organic shapeshifting monsters. Both have a Femme Fatale businesswoman associate whom they betray towards the end of the game. They even have a similar mode of speech and a tendency to keep their red eyes hidden.
- FaceHeel Turn: From a protagonist Anti-Hero who saved the city from a nuke during the first game, to god-complexed entity wanting to consume all of humanity.
- Fallen Hero: By the end of the first game, he was at least a Nominal Hero, and the lightest shade of gray in the whole sludgy mess. However, he ultimately ends up turning against humanity.
- Famous Last Words/"Facing the Bullets" One-Liner: "Huh. Welcome to the top of the food chain."
- Graceful Loser: Though he throws everything he's got at Heller in the final battle, he faces death congratulating Heller for becoming the strongest of all the Evolved.
- Hive King: In Prototype 2, he has taken Elizabeth Greene's place as the leader of the Infected.
- Hypocrite: Mercer described humanity as selfish creatures who only think about themselves. Before the final boss fight, Mercer performs a selfish act himself by absorbing his minions in order to power up himself.
- Jumping Off the Slippery Slope: Hoo, boy.
- He infects Heller, which Heller views as a curse.
- Ordered his Evolved to sabotage a cure for the virus.
- Said sabotage involves retooling it to spread the virus even further.
- In fact, the second outbreak was entirely his doing.
- Murders Father Guerra in cold blood to screw with Heller.
- He's driven Dana off to the point where she doesn't see him as her brother any more.
- Nonchalantly consumes his disciples (including Sabrina Galloway) to boost his own power for the final boss fight.
- And finally, he tells Heller to his face that he intends to make Amaya the next Evolved so that she can create more.
- Karmic Death: He shouldn't have kidnapped and tried to infect Heller's daughter.
- Killed Off for Real: Is consumed by James Heller in the final mission.
- Kick the Dog: Killing Father Guerra.
- Large Ham: He is much more "animated" this time around - gesturing grandly and making more of a meal out of his lines than his actual meals (which he seems to have given up).
- Laser-Guided Karma: After he consumes his remaining Evolved, he is consumed in turn by Heller, with whom he shared his powers early in the game.
- Manipulative Bastard: He has infected numerous individuals, called Evolved, with his strain of the Blacklight Virus and planted them in high-ranking positions in Blackwatch and Gentek to serve as spies. He also tries to manipulate James Heller into helping him out, but makes a crucial mistake that clues Heller into his real motives — mentioning that together they will destroy Gentek and Blackwatch... but not the virus.
- Motive Rant: Has one. Heller doesn't really care.
- No Sense of Personal Space: In his cutscenes with Heller (and in contrast with the first game), he has a habit of putting his hands on Heller's shoulders or chest as a means of seeming more sincere, and gets very... close with Galloway just before the last confrontation.
- Not So Different: Remember his disgust with Greene and his original incarnation? His actions in the sequel are near-identical to theirs. He even returns to Penn Station where the original Mercer was shot dead to release the virus a second time, apparently in the name of drama.
- One-Winged Angel: He spends most of the game appearing outwardly human, but when push comes to shove and after consuming the Evolved, his body becomes significantly more monstrous. Along with his old Shapeshifter Weapons distorting his form, his limbs become bloated and discoloured, spines erupt from his back, he's covered in blood, and his eyes glow red.
- Pet the Dog: Quite nice to Heller, at first — teaching him how to consume targets and gain memories from them and informing him that consuming the more monstrous Infected will give him new powers. He also never actually goes so far as to kill Dana even when she's trying to disrupt his plans wherever possible. Before his final fight with Heller, he hides both Dana and Amaya safely out of the crossfire.
- Pyrrhic Villainy: He really didn't need to take Heller's daughter in order to fulfill his plan, and this was, in the end, what got him killed, not that his Evil Gloating helped.
- Red Eyes, Take Warning: His eyes turn red during his fight with James Heller.
- Rogue Protagonist: In the sequel, his goals and mindset regarding the virus have changed.
- Social Darwinist: He believes the "Evolved", especially himself and Heller, are at the top of the food chain.
- Sudden Sequel Heel Syndrome: Went from a conflicted, guilt-ridden Anti-Hero at the end of Prototype to a megalomaniacal supervillain just in time for the next game.
- Snark-to-Snark Combat: In the final battle, Mercer and Heller hurl insults back and forth.Alex: Hey! I'm using that! (said if Heller uses the same weapon as him)
- Take Over the World: His goal in [PROTOTYPE 2] amounts to turning the human race into Evolved under his command in order to end all conflict.
- To the Pain: Vows this against Heller after failing to kill him:Alex: It would've been quick. But now... I'm gonna make you suffer.
- Villain Forgot to Level Grind: Implied. Alex has given up fighting in favor of more subversive methods, including creating and controlling the Evolved. During the final confrontation between him and Heller, instead of attacking with his Evolved as backup, he absorbs them to make himself strong enough to fight hand-to-hand — and still loses. Also, when Heller becomes a threat to his plans, Mercer tries to consume him, only to learn the hard way that Heller can not longer be consumed. He settles for killing Guerra in retaliation.
- Walking the Earth: Does this between games. He was very, very disappointed in what he saw.
- Well-Intentioned Extremist: His actions in the sequel are legitimately in order to end the stagnation and cruelty of humanity by killing most of it off and forcing the rest to become something... else. He's just... rather extreme about his methods.
- Would Hurt a Child: Makes explicit his intention to infect Amaya in front of Heller. He doesn't see it as 'hurting' her, and specifically made sure she'd be safe during the final battle, but if it'll piss off his opponent and cause him to start making mistakes... hey, whatever works.
- Zombie Apocalypse: His goal, expanded worldwide.
Sgt. James Heller
Voiced by: Cornel Womack
A marine who lost his family to the infection while he was away on duty. He returns to Manhattan, runs a series of suicide missions in the Red Zone, and is eventually mortally wounded. Mercer is impressed by his skill, however, and infects Heller with his unique strain of Blacklight. Now a newly super powered Heller vows to kill Mercer.
- Absurdly Sharp Claws: The first power James acquires. In its base form it has serrations on its back edge like a combat knife.
- Angry Black Man: Very angry, coupled with constant swearing.
- Anti-Hero: He's no white hat, but he's initially considerate of the civilian cost and disrupts Gentek's experiments on the populace. When Roland, a Gentek scientist and one of Alex's Evolved, mocks Heller for thinking he's a hero despite killing thousands to get at him. Heller's response:Heller: Did I say I was a fucking hero, you piece of shit?!
- Appendage Assimilation: Gains new abilities by tearing off and assimilating the limbs of Blacklight Abominations and Evolved with those powers.
- Badass Normal: Before his transformation, he fights his way to the middle of the Red Zone alone and kills a Brawler Hunter using only a combat knife. He also manages to land a few strikes on Mercer with no powers, though none of them actually harm Mercer.
- Batman Gambit: His long-running intimidation scheme for Galloway, which was useful for a while but panned out badly. In the various side-missions, Heller also manipulates Blackwatch, usually into exposing themselves to his attacks.
- The Beastmaster: Gains the ability to call Brawler Hunters to fight alongside him with the Pack Leader ability. He later also gets the ability to temporarily add Juggernauts to this arsenal.
- Blade Below the Shoulder: The Blade. Like the Claws, it has an army knife flavor in its base arm. Its size is even lampshaded in the game.
- Boisterous Bruiser: While he isn't quite as amoral as Alex started out in the first game, he is much more vocal in his enthusiasm.
- Civvie Spandex with a side of Magic Pants: As a shapeshifter and like Alex, Heller is technically not wearing clothing; his "clothes" are imitations that he created from himself.
- Combat Tentacles: To an even more extreme degree than Mercer. His Tendril powers can be used in conjunction with Wreaking Havok, allowing for wholesale devastation of scenery as well as large numbers of Mooks.
- Contrasting Sequel Main Character: Compared to the sullen, amnesiac, and somewhat easily manipulated former scientist Mercer who discovers he was never actually human, Heller is aggressively loud, retains his identity as a soldier, and trusts very few people that he doesn't have existing connections with while seeming happy to return to human life with his surviving daughter.
- Cursed with Awesome: Even he seems to realize this.
- Deadpan Snarker: Heller is an endless font of snark when he's not boiling with fury.
- Dead Person Impersonation: Courtesy of eating them and taking their form.
- Death by Origin Story: Or his wife anyway.
- Death Seeker: So he can rejoin his family, or so he says. Until he finds out his daughter is alive.
- Determinator: His first reaction to seeing Alex Mercer, super-strong super-agile notorious bio-terrorist scourge of New York? Pull out the only weapon he had at the time - a large knife - run up and slit his throat. He then charges Mercer and stabs him several more times, again without success. Even this did not deter him, and after chasing him across the Red Zone he still tries to stab Mercer, despite knowing it won't work.
- Did You Just Punch Out Cthulhu?: Kills and devours Alex at the end of the game.
- The Dragon: He was intended to be this by Alex Mercer. Didn't work out so well.
- Empowered Badass Normal: After the transformation.
- Emergency Transformation: He's unhappy about what Mercer did to him in order to save his life.
- Eye Beams: The Medusa's Gaze power granted by the Excessive Force DLC, which One Hit Kills anything and everything.
- He Who Fights Monsters: Present and invoked deliberately. To have a shot at taking down Mercer, Heller will have to become just as or even more powerful, and equally monstrous, which would be a hell of a feat. Due to the drastic changes in Mercer's characterisation, Heller does wind up defending New York from his hated enemy, though his humanity remains in question.
- Hopeless with Tech: Apparent in Mission 3, where he has trouble even reading the keyboard and doesn't bother logging off the computer he was using. While the keyboard did have a "triangle" key, and was thus no conventional computer, one gets the feeling that Heller's had similar experiences in the past.
- Hot-Blooded: James is very excitable, and often jumps into a fight without thinking.
- Horrifying Hero: Really hits home when he's finally reunited with his daughter and she's just too terrified to even touch him, since he's currently in Blade Below the Shoulder mode. She gets over it, though.
- Humanoid Abomination: Same deal as Alex. Except that he retains his human memories/identity.
- I'm a Humanitarian: Unlike Alex, Heller makes frequent, gruesome jokes about this ability and doesn't have the excuse of not actually being human, as Alex does.
- I Hate You, Vampire Dad: He blames Alex for the deaths of his wife and daughter and isn't pleased to be infected by Mercer.
- Immune to Bullets: With the "Bulletproof" mutation, he's immune to small arms fire, but not explosions or cannons.
- Instant Armor: The Armor from the Excessive Force pack. Subverted in that it's just a alternate skin and doesn't affect gameplay at all.
- Kill and Replace: Like Mercer, but his most prominent and lasting one was Lieutenant Riley, codename "Castle".
- Large Ham: He is both loud and extremely crude. His tendency towards Trash Talk results in a fountain of profanity, whether in battle or not.
- Lightning Bruiser: In the final fight against Mercer, he notes that he's just too fast for an enhanced and powered up Mercer to keep up with him. In the same fight, he also physically overpowers Alex. Also, in the first game, there were certain enemies who could catch Alex. Heller? Once he has all his speed upgrades, nothing can keep up with him.
- Luckily, My Shield Will Protect Me: The Shield, which can now be dual wielded.
- Made of Iron: Even as an ordinary human, he's able to simply shrug off getting tossed into a tank and subsequently getting hit with a Megaton Punch with enough force to create a Kung-Fu Sonic Boom by Mercer.
- Manipulative Bastard: Much like Mercer, Heller plays hail-Mary with Blackwatch command structure, and especially their field commander Rooks. Presumably, his own military experience facilitated his expertise with which he infiltrates Blackwatch. Likewise, he was able to milk Galloway for information for a long time, though that backfired badly when he stretched it too far.
- Meaningful Name: It's possible his surname of Heller relates to the Hela Cell Line taken from Henrietta Lacks. The cells are notably durable, resilient, and constantly strive to multiply.
- Papa Wolf: The sheer amount of hatred directed at Mercer as a result is truly frightening to behold.Enough of your fucking weird, fucking rambling SHIT. GIVE ME MY DAUGHTER!
- Person of Mass Destruction: Fully capable of destroying everything in the streets of New York in somewhere between an instant and a few minutes, by himself, somehow.
- Plague Master: An even better example of one than his progenitor, as he can infect his victims with a particularly vicious power named Biobomb. The afflicted are first engulfed in a mass of fleshy tentacles, then they are torn apart by the tentacles, which then proceed to impale unfortunate bystanders. He can also summon and control up to four Brawlers (depending on Mass upgrades).
- Power Fist: The Hammerfists.
- Scary Black Man: Considering his powers, they don't come much scarier.
- Shapeshifter Weapon: Mostly the same as his predecessor, but more organic-looking.
- Shell-Shocked Veteran: Was diagnosed with both PTSD and Unstoppable Rage.
- Shooting Superman: He goes after Mercer armed with nothing more than a combat knife, when Mercer survived a nuclear explosion.
- Sir Swears-a-Lot: Becomes noticeably much more vulgar after he loses his family.
- Smarter Than You Look: He's gruff as all hell and not always eloquent, which makes him seem a bit like Dumb Muscle. However, he's at times witty (though he ascribes to Black Comedy) and the way he turns Blackwatch upside-down makes it clear that he's not unfamiliar with subversive tactics. Being a sergeant in the Marine corps requires no little amount of intelligence. He also consumes a number of scientists throughout the game, gaining all of their memories.
- Spanner in the Works: Unwittingly at first, and then later intentionally, screws up Alex Mercer's plans to take over the world.
- Spikes of Doom: The Groundspike maneuver, now used in conjunction with the Hammerfists. His shields also become studded with spikes after a certain point.
- Superior Successor: Heller is in many ways superior to Alex at his peak, once you factor in all the upgrades. He's explicitly faster, stronger, and his powers are in some ways deadlier than Mercer's equivalents. About the only thing Mercer has on Heller is that Heller lacks Mercer's extremely jumping prowess.
- Super Senses: Viral Sonar.
- Super Strength: Even greater than Mercer's.
- Unstoppable Rage: His wife and his daughter (well, not the daughter) are dead, so he embarks on a Roaring Rampage of Revenge against the man he holds responsible.
- Villain Protagonist: He's in it for a Roaring Rampage of Revenge against anyone and everyone that pisses him off. He makes no attempt to disguise this fact and actively denies being a hero.
- What You Are in the Dark: Decides not to kill Rooks when he is on the phone and only they are in the room because he sees how he does care for his family.
- Whip Sword: Heller's Whipfist, while a Combat Tentacle, has serrations and is tipped by a blade.
- Why Am I Ticking?: The Biobomb allows him to infect and convert citizens into Action Bombs after a short delay.
- Wolverine Claws: The Claws, which bear serrations on their outer edges, similar to a combat knife. They can be used to perform a Deadly Lunge.
Dana A. Mercer
Voiced by: Lake Bell (Prototype 1), Lindsay Ames (Prototype 2)
Alex's younger sister and the first person he remembers after he awakes. A journalism student and spitfire with a sharp tongue and an inquisitive mind, she loves and idolises her older brother, despite not having seen him in five years, and acts as his intelligence gatherer and data analyst.
- Code Name: "Athena" in [PROTOTYPE 2].
- Distressed Damsel: A few missions revolve around rescuing her from peril. Pretty understandable, since she's not the one with superpowers or military training.
- Eerie Pale-Skinned Brunette: But only because she's always in the dark. She'd probably look normal in good light.
- In the sequel, she takes issue with being called "pasty".
- Et Tu, Brute?: Definitely her reaction in the second game when Alex imprisons her inside a bank vault with Amaya.
- I Have No Brother: Tells Heller to kill Alex after finding out he had Galloway kidnap Amaya, as he is no longer her brother, and explicitly tells Alex as he stuffs her and Amaya in a bank vault that Alex is "dead now."
- I Take Offense to That Last One!: In Prototype 2, a bunch of drunken soldiers call her and Heller up and insult them, calling Dana a "pasty hacker cunt." Afterwards, Dana gripes that she's "not pasty."
- Intrepid Reporter: Only a student, but according to her character profile, she's naturally inclined this way.
- Lady Swears-a-Lot: Though the entire game is hardly stingy with the F-bombs, she swears as often as the soldiers do.
- Mission Control: You get most of the story missions for the first part of the game from her. Continues this tradition with Heller in the sequel after Guerra dies, for approximately the second half of the game.
- Morality Pet: The only living being that Alex gives a damn about aside from himself. Also one of very few people in the game on speaking terms with stuff like ethics and sanity. Likewise, she is Heller's only friend and the only person he makes an effort to be nice to after Guerra's death.
- Now What?: How she ends the second game. "What do we do now?"
- Parental Substitute:
- Her character profile explains that this is the reason she trusts her older brother so absolutely; never knowing her father, Alex was the closest thing she had to a stable parental figure. Knowing this makes everything revealed about her brother roughly a bazillion times more depressing.
- Heller tries to convince her to take Amaya in if Heller is somehow not around. Though Dana's flustered, she and Amaya get along very well, and Amaya runs towards Dana when Heller's infection freaks out Amaya.
- Plucky Girl: Not that it does her any good given the setting, but this college-age girl with no combat training and no superpowers insults Blackwatch soldiers to their faces and actually headbutts one who put his hands on her. The fact that Alex splatted the guy a second later in no way lessens her sheer chutzpah. On the optimism count, she never turns her back on her brother, always helping him even when he's just gotten through explaining that he eats people, in the sincere belief that he's still in there somewhere and knows what's right. She's wrong on both counts — about her real brother. Her fake one, oddly enough, is less of a bastard and genuinely cares. In the sequel, though she's hardened a bit, she's probably the nicest character after Guerra's death.
- Scarf Of Asskicking: Sports one in the second game.
- Theme Naming: Her code name, Athena, is the daughter of Zeus in Classical Mythology... the latter of whom just so happens to be the code name for Alex, although it's never actually used in the second game.
- What Happened to the Mouse?: Rescued while unconscious, not seen again for the rest of the game. She shows up in the sequel as "Athena", Guerra's contact and Heller's second Mission Control.
Father Luis Guerra
Voiced by: Ivan Basso
A priest who runs the church in the Yellow Zone that Heller and his family once attended. He tried to meddle with Blackwatch's experiments, but failed and barricaded himself in his church. Heller snaps him out of his Despair Event Horizon and Guerra provides him with intel on Blackwatch supplied by a contact called Athena. Alex Mercer and a horde of Infected kill him after Heller becomes a threat to his plans.
- Badass Preacher: He's as compassionate as any priest should be, which does not mean he's averse to keeping an iron pipe close at hand should someone threaten his flock.
- Dark and Troubled Past: The guy knows a lot more than he should oughta about guerrilla warfare. Apparently, he's had a lot of tattoos removed.
- Meaningful Name: "Guerra" is Spanish for "war".
- Mentor Occupational Hazard: He's killed by Mercer.
- Revenge by Proxy: Killed by Alex Mercer and his Infected as revenge for Heller interfering with his plans for Whitelight.
Doctor Bradley Ragland
Voiced by: Phil La Marr
A pathologist who knows some uncomfortable secrets, content to run the morgue in a teaching hospital in New York. He once worked for GENTEK, but quit on ethical grounds some time ago. Dana sends Alex to him in the hopes that he can cure the parasite.
- Morally Ambiguous Doctorate: Good, but worked with McMullen in the past. Randall states that they have enough dirt on him to ensure he'd keep quiet.
- Only Sane Man: The only other character with a working sense of ethics.
- What Happened to the Mouse?: Alex leaves Dana in his care, and they both are not seen or heard from again afterwards. Unlike Dana, his fate is not alluded to in the sequel.
Director Raymond McMullen
Voiced by: Paul Guilfoyle
The Director of Research at GENTEK; Alex's ex-boss, who knows more of Blackwatch's secrets than is healthy due to his insatiable scientific curiosity. This fascination extends to Alex's abilities and eventually leads to his death.
- Better to Die than Be Killed: Especially when your enemy will gain vital information by killing you in a certain way.
- Evil Genius: For Blackwatch.
- Go Out with a Smile: He smirks at Alex just before blowing his own brain out.
- Mad Scientist: A subdued one, but he really wants to learn about The Virus, to the point that his curiosity gets him in trouble with Blackwatch because he keeps finding out things that they don't think he should know.
- Morally Ambiguous Doctorate: Yes, another one. He's evil.
Voiced by: Vanessa Marshall
Alex's ex-girlfriend and a scientist like him; her picture still hangs on the wall of his apartment. She helps him create a cure for the virus ravaging Manhattan. One of the viruses, anyway. Specifically, Alex himself; Karen was (possibly) forced into working for Blackwatch and the "cure" turns out to be a parasite designed to kill him.
- All Girls Want Bad Boys: Somehow, Alex won her over with his charming personality. Granted, she is his ex, but we don't know what went down or who dumped who.
- Boxed Crook: Downplayed, but WOI segments indicate she was detained by Blackwatch at or before the time the virus was released in Penn Station, and was given a choice of helping McMullen and Blackwatch manipulate Mercer, or... not.
- Dark Chick: For Blackwatch.
- Killed Off for Real: Not explicitly done ingame (though heavily implied), but in promotional materials for the sequel, they reveal that Mercer killed her.
- The Mole: Pretends to be an ally to Mercer, but she is actually being used by Blackwatch.
- Morally Ambiguous Doctorate: She was working for Gentek in the first place... however, she did attempt to talk Mercer down before Penn Station. She was captured by Blackwatch and given a choice between helping them stop the shape shifting, people eating monstrosity or being treated as an accomplice to Mercer's actions.
- Scylla and Charybdis: Presented with the choice between being on the front lines of an attempt to manipulate and destroy an Axe-Crazy Humanoid Abomination on a bloody swath of vengeance and hoping that doesn't come back to bite her, OR refusing to help the sinister Black Ops group that erases entire towns and hoping for the best.
Dr. Anton Koenig
Voiced by: Robert Morse
The lead virologist of Gentek, he's also in charge of its major projects in New York. Because Heller was infected directly by Alex Mercer, Koenig has taken a particular interest in him. He is one of Mercer's spies, having been infected with the same strand of Blacklight that gave him and Heller their powers, and was in charge of developing Whitelight - an upgraded version of Blacklight.
- Badass Grandpa: Thanks to the Blacklight.
- Blade Below the Shoulder: Like most Evolved, he can transform his arms into blades.
- Humanoid Abomination: One of Mercer's Evolved.
- Killed Off for Real: Dies very quickly.
- Mad Scientist: Pretty much a given, especially with the track record of other Gentek scientists. He is elated when he sees Heller is infected but alive — such an intriguing subject! Being an Evolved, he has other motives for investigating Heller.
- Manipulative Bastard: Plays Heller like a fiddle for a few missions, much like Karen Parker did to Mercer in the first game.
- Meaningful Name: König (of which Koenig is an alternate spelling) means "king" in German. He's the head virologist of Gentek.
- Too Dumb to Live: His betrayal of Heller? "Send more men."
- The Mole: For Mercer.
- Morally Ambiguous Doctorate: Given that he's the "lead virologist" at a company known only for creating some pretty deadly viruses.
- Playing with Syringes: The Gentek modus operandi, but his enthusiasm is unusual even for Gentek. He literally has Heller Strapped to an Operating Table at one point.
- Smug Snake: This guy perhaps has one of the worst cases of this, even amongst the Evolved. He tries to go against Mercer's orders and works to kill Heller simply in an attempt to gain his favour, and when the jig is up, he unabashedly admits hes been taking Heller for a fool and underestimates him at every opportunity. Even his final words before being pulped into the concrete and consumed by Heller is asking Heller in a sneering manner if he wants him to beg.
- We Hardly Knew Ye: He's an evil scientist. He's an Evolved. That's all we get.
Voiced by: Melissa Disney
The Chief Financial Officer of Gentek, Galloway is in charge of Gentek's financial affairs. She is also one of Alex Mercer's spies, having been infected with the same strand of Blacklight that gave him and Heller their powers.
- Blade Below the Shoulder: Like most Evolved, she can transform her arms into blades.
- Femme Fatale: She tends to rely on sex-appeal in order to get her way.
- HeelFace Revolving Door: Works for Mercer, being a spy in Gentek, but then helps Heller against Mercer's Evolved. Finally shifts back to Mercer's side when Heller consistently shows his contempt for her and doesn't take her offer to leave the city together.
- It's All About MeHeller: Who's side are you on?
- Humanoid Abomination: One of Mercer's Evolved.
- Manipulative Bitch: She's quite aware she's no soldier and relies on deals and planning to survive.
- The Mole: For Mercer.
- Rewarded as a Traitor Deserves: Consumed by Mercer along with the other Evolved present in order to supercharge himself for the final battle.
- Scarily Competent Tracker: Of other Evolved. She can track any of them, presumably by a method similar to Heller's viral sonar, except Heller himself and the untraceable Roland.
- Screw This, I'm Outta Here!: Tries to convince Heller to escape the city and leave his daughter behind. He doesn't take.
- The Sociopath: Her motivations are her own advancement and Gentek's bottom line, in that order, and absolutely nothing is off the table in the name of aiding those two things. She hopes Heller stops Operation Firehawk before anyone "important" is harmed. Heller immediately replies "I'll Pretend I Didn't Hear That".
- The Starscream: Suggests she and Heller team up against Mercer, but is rejected.
Officially designated the 1st Biological Warfare Command, Blackwatch is the government military force in charge of containing viral outbreaks. Their elite soldiers are handpicked from various Special Forces organizations, and each member is fully committed to stopping Redlight, no matter the means.
- Comedic Sociopathy: Their Sociopathic Soldier tendencies are often played for Black Comedy in Prototype 2.
- Elite Mooks: Blackwatch troops are this in the canon, but in regards to gameplay they're just reskinned Marines with slightly higher health (enough to absorb an extra bullet on the hardest difficulty, for how much that's worth). Their gunships are a more straight example, firing powerful homing missiles instead of just dropping off canon fodder like the Marine choppers.
- Faceless Goons: Literally and figuratively, Blackwatch troops have zero humanity. The sequel has some Blackwatch-aligned missions that puts a (figurative) human face on them.
- Flanderization: Blackwatch in the sequel are more or less a parody of their Prototype 1 incarnation (and well-intentioned extremists in general). Their first appearance post Heller's capture is a textbook Obligatory War Crime Scene, lining up a group of civilians to be shot for the subversive crime of spraying graffiti. One soldier gets a medal for "consistent display and embodiment of the organization's core tenets" after he shoots a woman for no reason.
- Fingerless Gloves: Despite the environment apparently being hazardous enough to warrant a gas mask 24/7.
- Gas Mask Mooks: Each one of them wears a gas mask.
- Goggles Do Nothing: They wear night-vision goggles during the day.
- The Man Behind the Man: To the Marines, directing things from their military bases while making the USMC handle the day-to-day duties. In the sequel they take a much more active role and seem, weirdly, to be Gentek's shock troops, rather than Gentek being their expendable research department as it was initially.
- Mission Control: A variety of mission controllers send orders out of the Red Crown Command building in Battery Park. A lone female controller, also going by Red Crown, takes over in the sequel.
- Repressive, but Efficient: They're actually pretty good at fighting the virus and would have stopped it several times had Mercer not sabotaged their efforts. Not so much in Prototype 2.
- Sociopathic Soldier: Literally a requirement; James Heller was rejected because he refused to shoot civilians. Desperate times demand desperate measures, though a lot of soldiers are extraordinarily eager to shoot anything that moves."I've gotta be fuckin' honest, if I had morals this would fuckin' bug me."
- Superpowered Mooks: Their super soldiers can go toe-to-toe with Mercer and Heller in fistfights.
- Unfriendly Fire: Done as a policy. One of their responses when getting patsied into shooting the wrong guy is "Do we really care if we're wrong?"
Captain Robert Cross
Voiced by: Jeffrey Pierce
A highly skilled and dedicated member of Blackwatch who believes wholeheartedly in what they claim to fight for: protecting the American people from the threat presented by the virus, whatever it takes. He leads a team of fellow veterans, the Wisemen, and has a reputation for surviving and winning battles with even the most powerful infected creatures.
- Arm Cannon: Sports an arm-mounted grenade launcher.
- Badass Normal: He fights Alex Mercer to a very close loss and walks away alive thanks to being Crazy-Prepared.
- Blood Knight: Randall tells him that ZEUS killed fifty men and smashed through a steel door as though these facts make fighting ZEUS a more appealing prospect. Apparently, they do.
- Crazy-Prepared: He uses Alex's flashbacks against him and make him vulnerable for a shot of the "Cure" (i.e. a parasitic cancer that blocks Mercer's powers). Unfortunately, it doesn't save him from the Supreme Hunter.
- Deadpan Snarker: Aside from cracking wise during his fight with Mercer, he dryly notes to Randall that containing Manhattan is "slightly" more than he and his dozen-odd men can handle.
- Defiant to the End: When he is about to be killed by the Supreme Hunter, he did not meet his end like a coward, instead readying himself and even intimidating the creature as it charges at him. Bad. Ass.
- Even Evil Has Standards: Since Operation Firebreak was not what he signed on for, he pulls a HeelFace Turn and tries to help Alex take down Blackwatch.
- Good Is Not Nice: Cross might be significantly less insane than the rest of his division, but he's Blackwatch to the core. He'll throw men at Mercer to whittle him down, speak worryingly casually about helping Mercer eat his superiors, and while 'allied' with Alex tries pretty hard to get him killed. All for the greater good, but yeesh.
- Guile Hero Antagonist: It may be a bit of a stretch to call him a hero at first, but he does manage to nearly defeat the Villain Protagonist Alex simply by talking to him and triggering his memories.
- HeelFace Door-Slam: Cross gets eaten by the Supreme Hunter well before he and Alex can stop Blackwatch.
- HeelFace Turn: Caused by the General's plan to nuke Manhattan.
- Inspector Javert: He's the soldier specifically tasked to capture Alex Mercer, but the motives for his Stern Chase initially avoid sympathy as they are dictated by Blackwatch. True to the trope description, he redeems himself when he teams up with Alex to stop Blackwatch from nuking Manhattan.
- Lightning Bruiser: Though the shock baton admittedly represents much of his damage potential, this man can dodge every blow Mercer throws at him so long as he isn't setting up for an attack with his arm-mounted grenade launcher.
- Manipulative Bastard: A close examination of Cross's late-game actions reveals that he plays Mercer like a fiddle.
- Not What I Signed on For: Which prompts his HeelFace Turn.
- Shock and Awe: He carries around an electric baton that can seriously hurt Mercer.
- Token Good Teammate: Unlike the other members of the organisation, who are fanatical at best and Ax-Crazy at worst, he has certain lines, like nuking Manhattan even when it is obvious that it is recovering a step too far.
- Sword Drag: Does one when staring down the Supreme Hunter, from its perspective.
- You Fight Like a Cow: Likes to drop one-liners about the player's performance during his boss fight.Cross: You might be fast, but I'm faster.Cross: Slow. Fatally slow.
- Younger Than They Look: He's thirty-eight. Really.
General Peter Randall
Voiced by: Gordon Clapp
The current leader of Blackwatch, directing their movements in Manhattan. He has been in the organisation long enough to remember Hope, Idaho, and the methods used to contain it.
- Authority Equals Asskicking: Not really. It's expected, since he's been fighting the virus virtually for his entire career and it was because of his orders and determination that Hope's infection didn't spread, but that was forty years ago when he had both arms. And indeed, when Alex finds him, he doesn't even go down with a fight.
- Cutscene Boss: When Alex finally catches the bastard, he grabs Randall, yells at him, and throws him down before casually eating him in a cutscene. Considering Alex's power by that point, the alternative was probably a Zero-Effort Boss.
- General Ripper: Randall wants to fight the virus however he can. If that means shooting innocent people, sending his men to die in a hopeless war, slicing his own infected arm off with a butcher's knife, nuking Manhattan and blaming the United States Marine Corps, or putting the virus in a position where it would do a huge amount of damage when it escaped to learn how to engage it properly, he will do it.
- The Unfought: You don't really fight him, but you automatically gain his memory node after the cutscene.
- Well-Intentioned Extremist: He says outright that he believes all casualties of any outbreak and resultant purge are "sacrificial lambs" necessary to learn how to fight the infection and "save the world" and may or may not have deliberately engineered the catastrophe that was the Manhattan outbreak, just to learn how to fight the virus on a larger scale. That this outlook and method are balls crazy and result in things like nuking Manhattan only after Greene is dead and the infection is weakening (because she couldn't then be retrieved for further study) seems not to occur to him.
Colonel Douglas Rooks
Voiced by: Daniel Reardon
The commander of Blackwatch operations in NYZ.
- Dirty Business: He's not a very good person, at one point sanctioning rape since to do otherwise would waste man-power and supplies. However, the game leaves him a somewhat sympathetic figure and surprisingly the Lesser of Two Evils, without denouncing his underlying mission of sterilization and control.
- Karma Houdini: Despite being in charge of Blackwatch operations, sanctioning very shady activities, Heller lets him live.
- Not So Different: He seems to realize this when he discovers Heller's daughter is still alive, realizing how he could use that against Heller and to his own advantage.
- Pet the Dog:
- Cares deeply for his own family.
- Lets Heller take his daughter and leave, though more likely because he recognized Heller is impossible to defeat, rather than because he was being nice.
- Pragmatic Villainy:
- Avoids shooting Heller when alone with the man himself, well aware that such an act would lead to a quick death and Heller, at the moment, has no real interest in killing him.
- Kills his own men so Heller can escape NYZ with his daughter, because trying to fight him directly had thus far proven too costly and ineffective.
Lieutenant Clint Riley
Voiced by: David Forseth
- The Dragon: To Rooks.
- Flyover Country: He's from a Midwestern upbringing, though his accent doesn't reflect it most of the time.
- Kill and Replace: Heller does this to him for a while.
- Not as You Know Them: In-Universe. Rooks manages to figure out that something is wrong with Riley because he acts... off after his encounter with Heller, and assumes he's a traitor. The truth is, in Rooks' opinion, much, much worse.
- Undying Loyalty: He hardly opens his mouth without having something good to say about or in defense of Rooks.
United States Marine Corps
The major military force on Manhattan during the outbreak.
- Artistic License Military: None of the vehicles they use during the game are actually Marine hardware. Their uniforms do not reflect anything used in real life, and Web of Intrigue cutscenes show them wearing Army uniforms.
- Earn Your Happy Ending: They're hailed as heroes at the end of Prototype (even if Alex was the one who did the crucial heavy lifting).
- Interservice Rivalry: A decidedly unfriendly version. The Marines regard Blackwatch as "baby killers," while Blackwatch call the Marines "amateurs" and "fucking dogs."
- Mission Control: They have their own mission controllers early in the game, who are gradually replaced with Blackwatch controllers. They're ordered around by Red Crown in the sequel.
- Punch-Clock Villain: The Marines are far less maverick than Blackwatch and more concerned with the lives of citizens.
- Red Shirt Army: Blackwatch use them as little more than cannon fodder to absorb the brunt of infected attacks; one Web of Intrigue conversation suggests that the only reason the Marines are there at all is to take the blame when Blackwatch nukes the city. It's even worse in the sequel, where literally all Blackwatch has them do is go on suicidal "patrols" either on foot or in open-air trucks.
Colonel Ian Taggart
Voiced by: Richard McGonagle
The leader of the Marines in Manhattan and Randall's second-in-command.
- The Brute: Although he doesn't look muscular...
- Dirty Coward: Or at least Randall and Alex think so when he finally snaps and tries to withdraw. But it's hard to blame him.
- Not that they're wrong, mind you. He orders an evacuation immediately after Greene is killed, causing military positions to collapse despite Greene's death weakening the Infected. Then he attempts to brute force his way through out of the quarantine zone despite this possibly spreading the virus.
- "Get Back Here!" Boss: He spends most of the time running away from you in his tank, while occasionally stopping to take potshots with its thermobaric cannon.
- Only Sane Man: In contrast to the above, he realizes right off the bat that both Blackwatch and the Marines are in no position to handle this threat, but Randall won't let him retreat.
- Too Dumb to Live: If you don't consume him in time, he'll try to drive straight through a Blackwatch quarantine barricade and get blown to smithereens.
- Villainous Breakdown: As the situation deteriorates, he tries to get Randall to deal with the problem at a distance. When Mercer comes for him, he panics and places his men between himself and the pissed off Humanoid Abomination coming to eat him.
- We Have Reserves: He begins throwing his troops into Mercer's path and certain death to gain time to escape himself. It fails, only succeeding in making Mercer really, really angry. He also wanted to perform Operation Firebreak on Manhattan from the very beginning in order to wipe out the infection from a distance, thereby exhibiting this idea for the enter population of civilians and other soldiers operating there.
Elizabeth Anne Greene/MOTHER
Voiced by: Kari Wahlgren
The last surviving inhabitant of Hope, Idaho, a town that was destroyed after being used as a testing ground for a biological weapon, to prevent the disease from spreading. She appears "burnt out" and catatonic after forty years of experimentation by GENTEK. There is almost certainly no remnant of "Elizabeth Greene" left; all that remains is the virus in an empty human host. Unfortunately, it is both intelligent and very patient.
- Ax-Crazy: There's nothing human left in her any more.
- Big Bad: One of the major antagonists of the first game.
- Cute Bruiser: Though the "cute" part is up for debate, she hits Alex once and he's smashed across the room. This is a guy who weighs hundreds of pounds slapped aside like a cardboard cutout by a teenage-looking girl.
- Decoy Damsel: GENTEK thinks they've contained her, and they're wrong. She's just waiting patiently to unleash the Zombie Apocalypse.
- Disc-One Final Boss: Her death doesn't end the game or the infection, though it does slow the infection quite a lot.
- Evil Matriarch: Her appropriate codename of "Mother" as well as being the origin of the Hive Mind invoke this.
- Hive Queen: Without a Runner like Greene or other directing force such as the Supreme Hunter or Alex, the lesser Infected remain mindless shambling zombies. However, with a Runner, it can think...
- Humanoid Abomination: She still looks like a 19-year-old girl. She and Alex share many similarities (strong, fast, resilient, power over the virus) but aren't quite the same. Only Greene was once human.
- It Can Think: And it is patient. If it's four years or forty years, the virus will wait in dormancy as long as it takes an opportunity to present itself, and during all that time, it plans. One mission revolves around Greene using infected people who haven't started showing symptoms as unwitting spies, their connection to the Hive Mind allowing her to receive information from them. After she dies, the outbreak loses its momentum almost completely.
- Latex Space Suit: Her clothing is outright modelled on fetish clothing and wet-suits, resulting in a skin-tight latex body suit with a lot of straps in weird places.
- Make Me Wanna Shout: In her boss fight, one of her attacks is a scream that sucks the colour from the screen and sends shockwaves over the battlefield that will knock you down to critical health if you don't move your butt.
- Not So Different: From Alex. This is especially played up when Alex takes her place in the sequel.
- Older Than They Look: She looks nineteen. She's actually over fifty.
- One-Winged Angel: Though it's possible she could have taken Alex in melee given the strength she demonstrates in the cutscenes, instead she dons a giant fleshy mass as armor and starts tearing everything around her apart. It takes a lot to bring her down.
- Plaguemaster: The virus spreads on everything she touches, and the Hunters, Leader Hunters, and Hydras are her creations.
- Sealed Evil in a Can: Or an observation cell. Then Alex accidentally lets her out. To be fair, she clearly could have left at any time, given the state of the room.
- Walking Wasteland: Everywhere she goes, the infection emerges, and her children follow.
- The Virus: By some quirk of biology, her body was mutated by the original strain to create viruses; hundreds of them. Every single one displays very strange properties. Gentek's reason for holding her is to examine and try to manipulate the strains into doing useful things, such as enhancing human attributes, killing people in specific ways very very rapidly, strengthening immune systems, or eradicating cancer, among other purposes. She's insanely valuable to Blackwatch because she is the only living subject to display the ability.
- Voice of the Legion: After she speaks, her words are repeated in multiple whispers.
The Supreme Hunter
After Alex removes the parasite, he attempts to kill Greene by using it on her, but her body rejects it. The result combines Mercer's and Greene's DNA and becomes something new: a creature with characteristics of both the Redlight and Blacklight viruses. It is not happy with its "father" for attempting to destroy it.
- The Dragon: To Greene.
- Dragon Ascendant: It becomes the de facto controller of the Infected after Greene is killed.
- Evil Counterpart: To Alex — roughly humanoid, just as smart (or smarter), same powers, and an independent entity, born from the virus and Elizabeth Greene but not under her thrall, just like Alex. Unlike him however, it wants to control and spread the disease and it isn't even a little bit human in body or mind.
- Evil Is Bigger: It's over ten feet tall, with bulk to match.
- Genius Bruiser: Its hideous appearance and lack of speech in its base form may make one think it's stupid, but it's anything but, pulling off a rather impressive Batman Gambit against Alex and the military, by taking the form, personality and voice of Cross.
- Humanoid Abomination: Especially when it consumes and replaces Cross.
- Kill and Replace: It killed Cross and took his place.
- Nigh Invulnerable: In its final incarnation, it doesn't even take Scratch Damage from 30mm cannon fire, AMRAAM missiles, Hellfire missiles, Javelin anti-tank missiles, or Alex's Blade power (which can slice clean through a tank). It takes a truly absurd amount of punishment to actually put it down, usually involving throwing huge numbers of 500+ pound bombs. It also regenerated from the first fight, where Alex reduced it to a puddle. It claims that, if it absorbs Alex, it'd even be able to survive a city-destroying nuke.
- Self-Made Orphan: First, it doesn't seem terribly distressed about Alex killing and absorbing Greene, its genetic "mother". Second, its purpose in life is to kill and devour Alex, its genetic "father" — implied to be at least in part because it resents him for not letting himself be eaten alive.
- Superpower Lottery: It has all of Alex's powers, but is stronger in every way.
Of all the children born during Hope, Idaho's infection, only one did not suffer fatal defects within months of birth. Codenamed PARIAH by the military, the surviving child was forcibly separated from his mother, Elizabeth Greene, and moved to a secure facility for study and containment. He never appears in the game, but plays a fairly large part in the Web of Intrigue.
- Bishōnen Line: PARIAH shows no sign at all of infection with the virus, and yet McMullen theorises that he could bring about the end of life as we know it.
- Blessed with Suck: Seems to kill anything he touches. As a result, he is kept either in a sealed cell or a courtyard surrounded by snipers and barbed wire.
- Creepy Child: There are three pictures of him. One is him playing with a ball, one is him playing with blocks, and the third is him standing beside a mutilated corpse with a handful of blood. What is this kid?
- Older Than They Look: He must be at least forty, but he looks no older than six or seven.
- Person of Mass Destruction: It's theorized by NPCs that if Alex Mercer and PARIAH ever came in contact with each other, the results could be beyond catastrophic.
- Sequel Hook: A hook is seemingly built up in the first game But averted in the second game; the sequel doesn't involve Alex looking for him. He is mentioned once as the assignment of Agent Barnes Griffin, and otherwise seems to have no bearing on events. But he's still out there...
- Super Prototype: In a way, Alex is the production model of what PARIAH is naturally, and probably isn't even as good. His powers were artificially activated, whereas PARIAH's are natural; PARIAH is everything the virus is meant to be.