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  • Catharsis Factor:
    • For one thing, after picking up a human-class entity, the only usual options are to either hurl them or eat them.
    • The statistics page in the game tells you roughly how much you've vented to date.
  • Common Knowledge: The story has a few holes and is rather arduous to see in its entirety, so players tend to go to the wiki to piece things together. Unfortunately, the wiki gets a lot of things wrong (often things that were mentioned in pre-release materials but dropped from the game), but the story presented there is probably more often-repeated than the one presented in-game.
    • There is no "Redlight Virus." The virus is always called Blacklight in the main story, and variants in the Web of Intrigue are specified as "DX-1118 [Letter]." Operation: REDLIGHT is actually the code name for the military occupation of New York. A trailer for [PROTOTYPE 2] which recapped the first game's story didn't mention Redlight and was criticized as being an example of the new writers' lack of respect for the lore, but the trailer was right and the fans were wrong.
    • Colonel Taggart is often stated to be a Marine officer but he's simply Randall's second-in-command in Blackwatch (the Prima guide describes him as "Commander of Ground Forces New York"). Hence why he wears a Blackwatch uniform, is able to order Blackwatch to evacuate, and his mooks during the boss fight are all Blackwatch troops. Even pre-release materials had him being a Blackwatch officer, it's not clear where this started.
  • Complete Monster: The real Alex Mercer was a cold-blooded Mad Scientist who bragged about making the Blacklight virus ten times as deadly as it already was. When asked how he felt about his work being used on human test subjects, he replied "Morality was not my job". Later, after being pursued by Blackwatch agents and cornered at Penn Station, Mercer decided to release the Blacklight virus on Manhattan as he was gunned down, despite being aware that his own sister was in the city at the time; this final act of callousness resulted in the deaths of over 10 million people. After discovering this, the virus itself expresses disgust with Mercer's crimes.
  • Crossover Ship: Alex Mercer is paired with Lucy in multiple fan arts. Probably due to their similar powers and personalities, they could make it work.
  • Demonic Spiders:
  • Difficulty Spike:
    • Let's be honest, there are points that will make you pull your hair out. Greene and the Supreme Hunter are the two big choke points, because they shrug off damn near everything that worked up until this point. It's downright vicious if you're going for the "No Deaths" Achievement. The final boss fight is easily the worst part of the game, because it's a timed mission that doesn't let you see the timer until it's half-gone and requires you to keep up a steady stream of damage to have any hope of winning, on top of the fact that the boss has an attack that will outright kill you if it connects.
    • Much worse in Hard Mode, which is Exactly What It Says on the Tin. Everything hits harder and can take more damage, to the point where bullets can actually do some real damage to Alex. You're going to have to earn that Achievement for beating it.
    • Hard Mode's first fight with Cross. No amount of practice in normal difficulty and prior play in hard can prepare you for the beatdown lying in wait. You'll find yourself forced to use tactics you don't normally use in Cross fights of lower difficulties.
    • Certain Platinum Medals are very hard to win, some more than others.
    • The first Hunter fight, as Alex doesn't have as much powers yet to deal with a stronger infected than the cannon fodder military and walking zombies.
  • Fandom Rivalry: There's only [PROTOTYPE] OR inFamous — apparently, you're NOT allowed to like both. Which is all the more ironic that the Devs went the Friendly Rival route.
  • Franchise Original Sin: Many fans will insist that Blackwatch in the first game is portrayed as an army of stone-cold Necessarily Evil badasses and lament their descent into Stupid Evil in the sequel, but they really aren't much better here. They accidentally developed a zombie virus as part of a plot to exterminate minorities; said virus gets released while they're trying to kill Mercer because he wants to leave Gentek/Blackwatch, and he wants to leave Blackwatch because Blackwatch is the kind of place that would kill you for trying to quit. They not only lose ground to the infected for the entire game but actively make things worse, and they're so deeply corrupt and disorganized that of the three major Blackwatch players one is actively sabotaging them, one is grossly incompetent to the point of collapsing the whole war effort by himself, and one sets off a nuke without bothering to tell anybody. Their only real success besides shooting civilians is making Bloodtox, which only pans out better than Whitelight does because Mercer personally babysits the last batch of the stuff. The only real difference is that Blackwatch gets more screentime (hence more opportunities for dog-kicking) in the sequel, and their inept violence is played for Black Comedy.
  • Friendly Fandoms: Retroactively gained one with Venom (2018), due to fans comparing how Venom's and Riot's transformation powers in the live-action film resemble a lot of Alex Mercer's moves and abilities from this game. Taking the plot of both titles into consideration, Venom can also be seen as a Spiritual Adaptation to [PROTOTYPE].
  • Game-Breaker:
    • The Blade, which is without question the strongest standard weapon in the game. Any blade attack in general does significant damage. A barrage of normal attacks with the blade will slice through tanks in under 30 seconds. Put on your armor and whip out your blade and you can slice your way through anything. A charged Air Slash move can one-shot Hunters, Super Soldiers, any kind of tank, and helicopters if you can manage to get above them. On Hard mode, it takes two. It tracks almost perfectly over significant distances, too. The charge time does leave you vulnerable, especially against tanks, but if you can get above your targets it isn't too big a deal. Recovery time can also be an issue.
    • The only real problem with the Blade is that it's kinda short-ranged... and that's where the Whipfist comes in. It has absurd range, good damage, and a Herd-Hitting Attack that can be charged for more damage. It sucks against armor, but one of its upgrades gives the ability to grapple in close to a target, meaning that now armored vehicles are one minigame away from getting hijacked (and whatever the Whipfist can't hurt, a barrage of helicopter rockets certainly can).
    • Helicopters, especially since most missions have Strike Teams which helpfully give you an infinite supply of the things. Both military and infected have no real way of dealing with you when you're in a chopper so they're an easy (albeit boring) way to cheese any mission they're available in. It's not a coincidence that most of the hardest missions have Strike Teams disabled.
  • Goddamned Bats: A number of things.
    • First, those damn virus detectors. Their high-pitched whine and very short sabotage period render them almost too much of a hassle to deal with, and they'll be in every army base a few missions after you learn they exist. Worse yet, they get more numerous as you progress, making it near-impossible to shut them all down without getting caught. UAV versions show up, too, which can detect you almost twice as fast and follow you even if you leave their initial scanning range.
    • Next is the helicopter Strike Teams, which are completely relentless. As you get stronger, they come in larger groups, and they eventually come with UAVs to detect you if you try to go sneaky. There can potentially be as many as four helicopters escorting five UAVs in the late-game. Even though they have to be called in by the military, the officers will do this within thirty seconds to a minute after you start a fight, and the window to kill the guy calling in the Strike Team is only a few seconds. What's worse, said guy can potentially be a tank. Thankfully, they're not terribly hard to kill, and it's even easier when you can skyjack the strike helicopters.
    • Third, there's the mid-level Infected civilians you usually fight during missions and events. Normally they're not so bad, just being about twice as tough as a regular Infected civilian and very fast. However, play during one of the events where you have to use a grenade launcher, and they are frustrating. They run around like they're on a permanent sugar high and will constantly run right in front of you just as you fire your weapon, resulting in you blasting yourself onto your back over and over.
    • In New Game Plus mode, it doesn't matter where you are - there are a couple of tanks on blow-up-Infected duty right around the corner and they always decide to turn down the street you're on. "Look dude, I was doing just fine cleaning up the Infected on this street all by myself. Why don't you try Lexington Avenue; I hear they're pretty thick over there."
    • Even when you have several powers that can slice through Hunters like butter, they'll continue to be a nuisance throughout the game simply for the fact they can chase you anywhere and can obnoxiously combo you up close if you let them. This annoyance is amplified during the boss fight against Elizabeth Greene, since three at a time will keep spawning and chasing you while you deal with One-Hit Kill shockwaves, thrown debris, homing attacks and having to run away to consume things for health constantly.
      • And during the minigame "events" that require you to kill a certain number of enemies in set amounts of time to get a Bronze, Silver or Gold medal, the ability of Hunters to enter a mode where they swing around blindly and cannot be blocked or stopped makes them frustrating beyond imagining.
  • Harsher in Hindsight: "My name is Alex Mercer. I'm the reason for all this. They call me a killer, a monster, a terrorist... I'm all of these things." Come [PROTOTYPE 2], and Alex, aka The Blacklight Virus is indeed responsible for the new viral outbreak and he is, indeed, all of those things.
  • Magnificent Bastard:
    • "Alex Mercer" is the Blacklight virus, which took the form and memories of the real Alex Mercer after he died. Awakening with no memories of his true origin, Alex starts to uncover it, thwarting Blackwatch operations along the way, saving and caring for his sister Dana, and even saving Manhattan from getting destroyed by a nuke. Growing disappointed with humanity afterwards, Alex decided to create a better world by wiping out humanity and replacing them with the "Evolved", people mutated with Blacklight which gives them similar powers. Creating the second outbreak by releasing the Blacklight virus upon New York and turning several people into Evolved, Alex had them infiltrate Blackwatch, which allowed him to manipulate the entire organization and use their resources for his own end. Infecting James Heller and turning him into an Evolved, Alex manages to briefly manipulate him and then corrupts the Whitelight cure, causing it to mutate people into Evolved instead of curing the virus. When James foils that scheme, Alex decides to kidnap his daughter instead, hoping to use her to infect the entire world.
    • The Supreme Hunter is the ultimate creation of Elizabeth Greene, who gained sentience after being defeated by Alex Mercer. Regenerating itself, the Supreme Hunter, at some point in time, tracked down and consumed Captain Robert Cross, taking his form and fooling everyone around it into trusting it. Manipulating Alex Mercer into eliminating key Blackwatch figures, before it used him to get close to General Randall to make sure Randall activated the nuke that was intended to wipe out Manhattan. Allowing Alex to consume Randall, The Supreme Hunter revealed itself to Alex, announcing its intention to consume Alex to empower itself to survive the explosion, to make the whole world to believe it is dead, while it can start to spread the virus somewhere else again.
  • Memetic Mutation: "You can do a karate kick on a helicopter! WHAT THE FUCK ELSE DO YOU WANT?!" Became an Ascended Meme during promotion for the sequel.
    • The above mentioned Precision F-Strike is answered with the other ability in-game that is equally as awesome, the fact that as Alex Mercer Really the Blacklight virus wearing him, Can and will ELBOW DROP A TANK AND WIN! In fact the tutorial section makes you do this.
  • Moment of Awesome: Almost everything you can do in this game. Kick a helicopter to death, throw a car at it, throw another helicopter you just shot down at it, throw people at it... the possibilities are endless.
  • Moral Event Horizon:
    • The real Alex Mercer, both for his work in making the Blacklight virus, which was nasty enough before he got there, TEN TIMES as lethal as before. Also for unleashing it when cornered by Blackwatch after he stole a sample.
    • Blackwatch infecting Hope, Idaho for no better reason than to test out the virus on people.
  • Narm: "Taggart! You suicidal moron!" Really, every all-caps line from Alex during that mission. Very, very well summarised in this Youtube Video.
  • Player Punch: Congratulations! You're The Virus! As an added bonus, even though you're a deadly virus specifically designed to kill people on a massive scale, you're a better person than the original Alex Mercer!
  • Porting Disaster: For the PC, Prototype is very picky about what qualifies as "recommended system specifications". The game only has very limited video settings. It even struggles with maintaining a double digit frame rate on the menus, not to mention in actual gameplay. There were also issues with audio sounding exceptionally muffled even at supposed normal volumes and other issues. Definitely not one of the best ports out there, especially for low-end machines.
  • Special Effects Failure: The game lacks an enter/leave animation for drivers (said drivers are in low resolution), most noticeable with the squad car where the driver will not get out unless the camera is off-screen.
  • Scrappy Mechanic:
    • What's so unique about Hint collectibles when they can provide a hefty EP like the Landmark collectibles? Well, Hints give gameplay hints, information that the player may have already knew while playing the game naturally. These became somewhat of a moot when you've unlocked everything else aside from the collectibles - The "hint" would be just redundant with the Loading Screen tips, and the EP can no longer be used once you've fully upgraded Alex.
    • The fact that you get stunned by almost every enemy's attack can be infuriating, especially during combat events where every second is crucial. The time it takes to recover from a missile or tank shell hit can easily screw you out of a gold or platinum medal.
  • Sidetracked by the Gold Saucer: The optional side-quests in this game may seamlessly blend together while you are in Free Roam, which becomes distracting while doing the parkour events. Reaching for that next checkpoint but then notice a nearby Landmark/Hint collectible that you've recently found and a Web of Intrigue citizen just respawned? There's nothing stopping you from accomplishing both while in the middle of the parkour Event (except from trading time). Only the Gliding Events put some restriction on this, as they end once you land from a glide/jump.
  • Spiritual Successor:
    • To Radical's The Incredible Hulk: Ultimate Destruction. One who has played both will easily notice that the gameplay remains the same for the two games (moreso than your typical spiritual successor), and a good deal of mechanics and moves have been retained... in fact, let's just call Prototype a sequel in gameplay only.
    • Word of God supporting this: The guys at Radical got the inspiration for Alex Mercer's shape-shifting abilities while playing Ultimate Destruction and using the Hulk's "weaponize" skills. They asked themselves, "What if [the character] could weaponize himself?" and an idea was born...
    • Also a successor to the Ultimate Spider-Man game, in a way. The two were developed by the same people, and it's impossible to not notice the similarities if you've played the other one. Alex's running animation is identical to Spider-Man's. His charged jump is identical to Venom's superjump. His throw is identical to Venom's throw. Finally, his tentacle attacks are identical to Venom's tentacle attacks... except for some of the Devastator moves, which are identical to Carnage's attacks.
    • In large part also to Spider-Man 2: The Movie, the game. The setting in Manhattan, the Landmark objectives (although the Spider-Man ones only gave a Bragging Rights Reward), the various optional events to collect points, the Le Parkour gameplay, the Wide-Open Sandbox world, these can all be traced back at least this far.
    • This game is rather similar to Spiderman Web Of Shadows, which came out approximately a year before this game. Both games are by Activision, both start with A Taste of Power shortly before the plot ends, both have a Zombie Apocalypse going on in NY, in both cases it is the fault of the protagonist to a certain degree, in both cases the protagonist gains dark/evil powers. Even the attacks are very similar, with combat tentacles, body surf attack etc. The Symbiotes are even pretty similar to some of the infected and Spidey's black suit's gameplay and attacks are rather similar to Alex's attacks in the game. Heck, the two games even have a similar plot: New York, or at least part of New York, is under quarantine for an epidemic that gives people superpowers but also turns them into monstrous creatures. Spidey and Alex are both infected (Spidey with his black suit, Alex with Blacklight). Venom and Elizabeth Greene even have the same goal: To infect the entire world. Also, the final boss battles of both games both take place on a gray-colored military ship/carrier of sorts. Both games also take place in a free roam open world environment and both New Yorks get more and more apocalyptic as the game goes on, which gives them a rather similar background esthetic.
  • That One Attack: The Tendril Barrage. Not yours, but courtesy of the Supreme Hunter, because it can kill you no matter how high your health is and bypasses your Last Chance Hit Point.
  • That One Boss:
    • The second battle with the Supreme Hunter, aboard the Reagan. It wouldn't be so bad (big guy throws out an attack you can dodge, then hit him while he's recovering), except he's constantly getting shot at by aircraft, helicopters, and rocket-toting soldiers. This does next to nothing to him. But if you try to attack while a missile hits, you'll get knocked back and a decent chunk of health is knocked off. Depending on your luck, it ranges from frustrating to inducing the paranoia that the boss and military are working together to piss you off. The time limit doesn't help either. In Hard mode, the fight gets even more annoying because That One Boss is constantly blocking many charged attacks and happily uses new abilities copied off you such as the ground spikes. Throwing stuff still works, though.
    • Hard difficulty makes every boss That One Boss. Even Cross, the very first boss, becomes a nightmare to fight, if only because the delay between firing and going into counter-mode is vastly shortened, his grenades have a much larger explosion radius, and he both reloads and fires a whole lot faster.
  • That One Level: The three levels where you're infected with the parasite. Imagine the level where you first meet the Hunters times three. The only thing good about the parasite section is that its ending gives you slick armor and the blade.
  • That One Sidequest: Getting Platinum medals.
    • The "Raid" War Event, which requires a time of 1:25:00. For every other event, getting Platinum is mostly a matter of skill (or cheating). Not here. You have to use a grenade launcher, so no powers, and there's 18 Hunters out of 36 enemies to kill. Moreover, the spawns are woefully screwed up. The game will sometimes withhold new targets for as long as 15 seconds, and just to spite you, it will do this on the very last enemy. If that weren't bad enough, it is impossible to succeed on your own. You have to count on a tank spawning to help. Just like the enemy spawns, it is completely unreliable, and you'll be lucky if this thing even shows up until halfway through. Assuming it does, you have to hope Hunters are the only thing on-screen for it to shoot, that it doesn't get bogged down in traffic, and that the Hunters don't gank it on sight before you can get their attention. It's a Luck-Based Mission.
    • "Kill: Street Sweeper" is just as luck based, but also requires much more precise positioning of Alex, lest you not get the kills needed.
    • All of the movement events except for Free Running and Corners (if you know the trick; double air dash in the streets while heading to the 2nd last and last checkpoints). Precise movement is required, with an analog stick at that. In most cases, one small mistake will cost you, and there are plenty of opportunities for a mistake. The worst two offenders are Eaves Jumping and Rooftop Runner. In the former, it's mostly a simple path, except you must run and airdash along narrow rooftop, and moving Alex to the side for a moment, even while not airdashing can cost you. The latter requires several sharp turns, with the camera being not too cooperative in helping you aim as you turn.
    • "Kill: Irony", not because it's difficult to get the points (you can cheat by blowing up a line of hijacked tanks for free points), but because the weak APC is likely to get brought down by RPG-toting soldiers before you can complete the mission and actually get credit for it.
  • What Do You Mean, It's Not Symbolic?: The level in which you fight the Supreme Hunter while a nuke is counting down is called One Thousand Suns, a reference to Robert Oppenheimer, who was himself referencing (or at least thinking of) the Bhagavad Gita, Hindu scripture, after the first successful test of the atomic bomb at the Trinity site (during what was, for extra fun, called the Manhattan Project). In three words, the developers crammed references to world-destroying superweapons, scientific progress and consequences, the phrase "I am become Death, the shatterer of worlds," a religious quote, and two puns... Or maybe they were just talking about the nuke. It's hard to tell.
  • The Woobie: Dana. She's one of the few characters in game who isn't evil or insane, her first scene in the game is a Blackwatch goon threatening to kill her, and things get progressively worse for her from there.

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