Prototype 2/Headscratchers

Folders for preventing spoilers.

Alex and Dana

 * Okay, in this game, it's fairly clear Alex and Dana hate each other. Dana thinks Alex is a monster rather than her brother, while Alex releases a virus into Manhattan while she's still there (mirroring the human Alex Mercer, who was far more evil than Blacklight Mercer was at his worst), locks her in a bank vault, and seems to blame her for something that's never explained. I... have an even harder time imagining this happening than Alex's Face Heel Turn in general. The first part of Alex's Character Development in the first game was starting to actually care about Dana as something other than a source of information. Even when he was still willing to let the rest of the world burn for the sake of his vengeance, he wanted her safe. She was his Morality Pet, and I have a hard time imagining the Mercer from the first game suddenly not caring about her, even if he were to turn evil.
 * Dana outright claims that Alex isn't her brother anymore citing that there was once a young man named Alex who, "played games with her, went skating with her, and would watch scary movies with her", and that the loving brother she once knew is dead now and all there is now is a monster in the image of her brother. Alex claims that all the animosity between them is of her own choosing and that in his new viral form he has risen above such concepts as "life" and "death" and that what has happened to him is a gift, not a curse. Even after all that Alex never kills Dana even though he could crush her like a bug, Dana is still Alex's morality pet as he simply wanted her on his side.
 * What I find most interesting is that he never made her an evolved.
 * Maybe she didn't want to become one, and Mercer didn't want to force his will on her (at least not at that time).
 * Problem with the interpretation that he still cared about her—he released the virus in Manhattan when she was still there. That was likely to kill her no matter what else happens. It's kind of the thing that the original Mercer did that proved he didn't care about her or anyone else. Not to mention that the idea that the virus is a gift is a complete reversal of his stance in the original game, where he characterized himself as "less than human" because of his status as a viral entity—he was sure as hell glad not to really be Alex Mercer once he found out what the real one was like, but he took a dim view on the fact that he was something made to consume and infect and destroy.

Why are the Supersoldiers Treated as a New Thing?

 * So, why exactly are the Orion Project Super Soldiers presented as being a newly developed thing, when Blackwatch had Super Soldiers in the first game over a year ago?
 * I think the implication is that these ones are somehow different (and strong enough to take on Heller's level of power), as shown by how they had "Phase Twos" in development.
 * The Orions are more powerful and dangerous. Its not so much that the idea is new, but that the Orions are much more dangerous than the old version.
 * Really? I could've sworn the original D-Codes were much harder to beat, rather than the suplex fodder that is Orion. Plus they all had inborn viral detectors.
 * I had absolutely no problem killing the D-Codes. Theyw ere slightly more challenging Hunters. The Orions are much harder to deal with.
 * I think they were trying to imply that Heller was stronger on all counts than Mercer. Hence why the "new" Orions are the same strength level approximately but seen as newer and better.
 * So what's with the Orions not being able to detect infected nearby like the original D-Codes? Blackwatch seems to have reloaded their concept of viral detectors, now being unable to be sabotaged so easily. So why not extend the concept to improving Orion awareness?
 * Well, the Orions weren't exactly done. Maybe that part of the Orion Project hadn't been completed yet before they had to start pushing them into battle?
 * Also, keep in mind that Koenig and his team had a hand in the project. Something tells me that giving the Orions the ability to detect the infected probably would not be a very high priority for them.
 * They're also new in the sense that neither Heller nor Guerra is aware that they existed. There may have been rumors of their presence before, but neither of them had encountered the originals, let alone the Orions.

Alex's Face Heel Turn
Okay, so we PC gamers don't get this for awhile, so I'm not gonna even try to avoid being spoiled, but what's with you-know-who's Face Heel Turn? Wasn't he at worst an Anti-Hero at the end of the first game? "Alex Mercer: "My name is Alex Mercer... They call me a killer, a monster, a terrorist. I'm all of these things.""
 * The prequel comic duology, The Anchor, explains that after the end of [PROTOTYPE],  travelled the world trying to regain his faith in humanity, only to discover that Humans Are Bastards everywhere he goes. For more extrapolation:
 * I'm certain he saw a hundred worse things in Manhattan.
 * While he may have seen worse things in Manhattan, that was kind of the result of the massive self-aware viral infection and the psychotic military force sent in response. In this case, Mercer is encountering ordinary people away from insane crises like the aforementioned.
 * He infiltrates towns under the control of drug barons, enters combat zones and civil wars. And Blackwatch is utterly human. Hope was a "progressive" project that took entire families, infected them, built a town for them and then watched to see which of them would die first and how. If humanity's cruelty is the reason he decided we were worthless, why the heck did it take him that long? Just how slow on the uptake is he supposed to be? (And why does he think the virus is any better? His strain was designed to kill, absorb, copy and infiltrate living beings - in short, it's backstabbing-in-a-beaker. Even Greene's strain saw the lesser Infected being used as resources by the ones higher up on the hierarchy.) At some point, the logic stops being a failure on the character's part and starts being lazy writing.
 * Forget that. Doctor Ragland from the first game worked for Gentek until he had an attack of conscience over their work.
 * We don't know what Ragland actually did while at Gentek. all we know is he refused to work on BLACKLIGHT. Gentek might of had some less then evil projects at the time
 * Let's just pretend this Mercer was a clone. It's better that way.
 * I can understand Mercer viewing the virus as the next step in human evolution. One has to admit that the kind of powers that Alex Mercer possesses are incredible and would be desirable for anyone to want to have. However the problem I have with it is that Mercer was trying to force this evolution using a mass infection that nearly destroyed New York 2 years prior, the same New York that he heroically saved from Gentek erasing it off the map with a nuke. Ideally he should have examined what makes the virus in his body tick and isolate the desirable shape shifting powers he has and remove all the Zombie Apocalypse, Eldritch Abomination stuff about the Blacklight Virus. That is far more sensible than condemning millions of people in New York and billions more if it spreads outside of New York to death and mutation.
 * Even given The Anchor, his methodology really doesn't make any sense. For these reasons, he decides   If he had thought that through some more, maybe We Could Have Avoided All This.
 * Keep in mind that Alex ate Greene, Randall, and hundreds of Blackwatch troops and scientists. I doubt he is entirely sane or rational at this point.
 * In the first game, upon Alex's realization that he is "not human" and that Alex is "just a role [he] plays", what made him want to connect with humanity like the Anchor comic would seem to suggest? Does it have anything to do with Alex being "something more" despite being "less than human"?
 * Okay, even with the explanations above, I still have a problem with this. For one thing, it's an abrupt and bizarre reversal of his entire character arc for the first game. His entire character development revolved around growing a conscience, learning to care about others, and growing into more of a genuine hero, culminating with his saving Manhattan in what could have been a Heroic Sacrifice if he hadn't proved so resilient. Second, even disregarding the sudden reversal, how does he go from deciding that for all his power, he's a subhuman monster—as a viral entity that exists to feed and infect and destroy—to deciding that the world would be totally better if everyone was like him?
 * I'll tell you why. To make way for James "I am generic revenge-seeking tough guy" Heller. It seems that, in an effort to improve upon the original, they thought that getting rid of the hero was a good idea.
 * This is sort of the crux of the entire argument. Mercer had already gained so much power that he was more or less invincible (to the point where not even trying to Nuke'Em actually killed him). It wasn't about "making him think humanity deserved it" in the case of the comic. It seems more like they simply believed that Alex Mercer could not be improved upon any further to validate a sequel. Not as a fan of one series over the other, but their supposed "rival" series seemed to do well enough at that by disabling some of their main character's more advanced abilities and giving a different, more powerful antagonist to necessitate gaining new powers (in this case, perhaps a better Stealth Consume, the other Mutations you can gain, Biobomb, Pack Leader, Viral Sonar, and Tendrils, among perhaps upgraded vehicles). Apparently in the case of this series, they didn't consider that option, hence what many consider the Sudden Sequel Heel Syndrome.
 * Mercer wasn't invincible, the nuke would have killed him had he not gained enough distance away from the explosion, besides powerful viral entities like the Supreme Hunter are capable of consuming him and enough damage from conventional weapons can still kill him in game play. Besides there is still the threat of PARIAH that would have validated Mercer becoming even more powerful than ever before, the first game had a ton of foreshadowing how if Mercer and PARIAH ever met it, "could be the end of the world." PARIAH could have been like The Beast from In Famous, an overshadowing threat that the protagonist must prepare himself for to save the world, The Beast is foreshadowed in Infamous and then appears in Infamous 2 justifying Cole's increase in powers. For a so-called rival series Prototype didn't follow that model very well. James isn't as invested in the back story and overall story arc of the game as Alex Mercer is.
 * If they felt Mercer was so powerful then what the hell will they do about Heller if they do a third game? Make him evil? Because any other option they go with will have people asking why they didn't do that with Mercer.
 * Regarding the comic book that elaborated on the time spent between the original Prototype and 2; are we honestly supposed to take the  seriously? How can Alex Mercer have anything resembling a normal human relationship   and spend his life casually with all these powers? Was he expecting the white picket fence life style where   he just gets to settle down and not have to worry about the horrifying implications of what his powers have done to his humanity? I find it silly that he would even think along those lines when he claimed that he had become something, "more than human", and even more silly that his face heel turn is based off of things ending badly with   one bad experience ruins his entire perception of humanity that's good writing.
 * Going off of that, wouldn't he have learned his lesson from from the original Mercer and not  again? This is a man-shaped creature who has developed true empathy...but.
 * I viewed what happened during the Anchor as being what finally pushed Mercer over the edge. It's not that he based his entire view of humanity around what they did. It's just that it was enough to finally cement his already spiteful view of humanity.
 * So Cross didn't matter? Dana didn't matter? Ragland didn't matter? And the virus - his "true" family - wasn't exactly welcoming. Greene told she was his mother, yes, but she smacked him around, kidnapped his sister, and then smacked him around some more. And the Supreme Hunter manipulated and betrayed him as effortlessly as anyone else. Sure, what happened in The Anchor was awful, but it's an incredibly weak justification for the viewpoint "Humans are scum because all of them are out for themselves. I will use the virus to make humanity perfect." Not at least because that viewpoint isn't even properly borne out in his actions. His Evolved betray him and bicker among themselves, his favourite ate him, and despite their otherwise slavish loyalty they don't exactly come across as having "one body, one mind, no suffering." It's just so...inconsistent. Non sequitur. It does not follow. (Especially because he keeps acting like he's still the original Mercer and was changed like Heller, instead of what he really is. No mention is made of that reveal at all.)
 * Cross died long before Mercer got to know anything about him, Ragland isn't mentioned, and Dana no longer considers Mercer to be her brother. The latter of which he locked in a vault instead of killing. So it's not as if Mercer has decided to kill everyone. And about the "One Body, One Mind" thing. It seemed as if that was only going to happen once Mercer spread the virus around the world via Whitelight. One memory stated that Mercer would have been able to control every drop of 'contaminated' Whitelight, even down to it's molecular level.
 * That's the thing. So much isn't mentioned. Why doesn't Dana think Alex is her brother any more? She seemed completely convinced of his good intentions in the first game and he willingly played into her beliefs. What happened to Ragland? The very last we see of him, he was taking care of Dana. This isn't about Mercer wanting to kill everyone, it's about his weird reversal of values over such a strangely petty thing and there is very little examination of the lead-up or aftermath. Just the effect. Alex is just...suddenly villainous, and takes on villainous mannerisms that he never exhibited before. As above troper said, he may as well be a clone or an evil twin.
 * Does it have anything to do with this quote?
 * Does it have anything to do with this quote?


 * No, not really. Alex was never a good person. We know it, he knows it, everyone knows it. (And Heller is no better; he says so.) Alex is violent, ruthless and bloodthirsty. But he wasn't megalomaniacal, and he did not want the virus to spread even when he found out he was it. Alex was far more of a conflicted Anti-Hero who, to paraphrase V for Vendetta, was born from something monstrous which thus made him a monster than he was the Weskalike he's characterised as in the sequel. He feels guilt for his deeds, he's outright disgusted at Blackwatch for their hypocrisy, he's relieved when he learns he's not human because the human he was once condemned millions to death...he knows he's a bastard, but that doesn't mean he couldn't recognise other bastards or want to punish them.
 * Though looking back at the quote after P2, it's either amusing or somewhat disturbing.

Pariah
So they didn't do anything with the sequel hooks from the first game? Nothing about Pariah, or the true nature of the virus? Kinda disappointing.
 * One Agent Barnes Griffin (a consumption target late in the game) has his name mentioned as being currently assigned to "Project Codename: PARIAH". That's pretty much it. It's in those "file-flipping clip show" type things while someone talks about someone else, and doesn't even get a direct mention in dialogue.
 * Maybe there saving it for a sequel?
 * PARIAH is currently sitting in some military base far away from NYZ. How would they involve him?
 * The same way Alex went globe-trotting between games despite being the most wanted terrorist ever?
 * Wait, PARIAH wasn't supposed to be the explanation for why Cross was suddenly a super-powerful Infected at the end when he'd previously been a seemingly normal human? Wow, totally misread that one.
 * I originally thought that too but it actually turned out that the Supreme Hunter simply absorbed Cross. PARIAH is still in Gentek custody.
 * It is. There's a cutscene that heavily implies they fought, and he's not seen in the flesh until the final battle of the first game. Pariah is still in custody.
 * Or more likely, still in Blackwatch custody, since a memory concerning an exchange between Randall and McMullen reveals this.
 * That still brings into question what agency Barnes Griffin works for. It's unlikely that they'd have agents in plainclothes go into a war zone.

Why is Heller so Powerful?

 * How is it that James Heller becomes so powerful that he can fight on par with  Alex Mercer? Mercer has had control of these powers of his for 2 years now so he should have considerably greater speed, strength, and endurance in comparison to a guy that Alex himself infected only a short time prior. Also what about Elizabeth Greene and the Supreme Hunter, not to mention the hundreds or maybe even thousands of infected he consumed? None of that did anything to increase his already Physical God power?
 * It seems plausible that he lost a sizable amount of biomass when "Operation: Firebreak" (the nuke) detonated. He seemed to barely be able to consume the raven to regenerate. Furthermore, he used his own biomass to recreate the infection, and see how big that was. He also had an A God Am I complex by the time they met. Maybe he thought he couldn't' be beaten, being "the top of the food chain". It does seem odd that he wouldn't develop mutations that the Blacklight Abominations and had and more, and that "supercharging" himself didn't really help, but there's also the problem of gameplay consistency. If one would go on the idea that he can  given more experience and time than his opponent, there's also the idea of  If we were going on feasibility, the fight would have been longer and hopeless, either a Hopeless Boss Fight or Heads I Win, Tails You Lose.
 * It seems likely that Mercer stopped aggressively evolving and instead shifted his attention to being the leader of the Infected; any mutations he engaged in likely involved directly controlling the Infected over direct combat. His subordinates developed their own mutations while working out in the field, but Mercer himself didn't need to mutate any new combat powers or abilities. Heller, meanwhile, is aggressively developing his combat mutations in the field by constantly fighting Blackwatch and the infected and absorbing powers from Mercer's minions. That, and he's really fucking pissed.
 * So essentially, Alex stopped gathering personal combat strength in favour of expanding his army, where Heller spent pretty much all the time up until they fought gathering personal combat strength. Even with the boost provided by consuming the Evolved, and given Heller's extreme emotional investment in winning (which Alex lacked), Heller simply outmatched Mercer. Though given Alex's last line and the way the virus works, one has to wonder if it wasn't a Xanatos Gambit. Either Alex consumes the Evolved and Heller, thus gaining the power of them all combined, or Heller consumes Alex along with the Evolved and proves himself a worthy successor. Gives a new dimension to the taunt about infecting Maya, for one thing. Enraging Heller into going all out...
 * I was expecting that reveal from the start, and was confused when it didn't happen. The idea that this was all an elaborate ploy to groom a successor makes a hell of a lot more sense than "Remember how Alex's entire character arc in the first game was about growing from a vengeance-fueled sociopath into a genuine, if dark, hero? Forget all that. He's totally evil now."
 * Heller was a highly-skilled and incredibly confident melee fighter even before his infection - when stranded in the Red Zone he didn't even bother looking for the shotgun he must also have been carrying, preferring to rely on his combat knife, and then he managed to kill a Brawler single-handed. Mercer, on the other hand, was a scientist (not that he even remembered that). Even given Mercer probably ate a lot of people with the same amount of training as Heller had, maybe the actual lived-through experience is more valuable than just getting the knowledge second-hand from some poor sucker's brain?
 * Human powers are a lot different from viral induced powers like shape shifting, super strength and speed. Mercer should have much greater mastery over those powers than James does. Even without that keep in mind that experience should matter. Just as a human Mercer would be a noob as a fresh Marine compared to a human James that is a war veteran and has experience as a Marine, a fresh viral James should be a novice compared to a veteran viral entity like Mercer who has had these powers for much longer.
 * As noted above, Mercer has seemed to be focusing his powers less on direct combat and more on controlling the Infected. Heller, meanwhile, has been focusing on both strengthening his own abilities and consuming the powers of Mercer's subordinates. He's simply evolving and mutating faster, and remember that Heller started close to where Mercer was at the end of the first game (he has most of Mercer's abilities, save for activated powers) and he only gets stronger.
 * Doesn't that make James Heller pretty Sueish? It just doesn't seem realistic that he could mutate at a faster and more explosively powerful rate than Mercer was capable of in two years. I call huge Game play and story segregation on this nonsense, I bet if we were playing as Mercer he would have won the fight no problem.
 * No, it doesn't make Heller "Sueish" because there's a lot more to being a Sue than just "character is more powerful!". (that and Mary Sue is so distorted by now that it has as much relevance to characterization as custard pie has to railgun research. Use a real term to describe a character!) I just pointed out why it would make sense: Heller started close to where Mercer was originally, and Mercer hasn't been aggressively improving his combat abilities and focusing on controlling the Infected, and Heller has been aggressively eating all of the Evolved with new and unique mutations to rapidly make himself stronger. Mercer's greater experience is reflected in his ability to control the Infected. And what do you mean, "it doesn't seem realistic"? We're talking about a fictional supervirus that alters biomass to allow you to tear apart tanks, leap over buildings, and telepathically control millions of infected zombies and mutants. Going on about things being "realistic" is ridiculous when we're dealing with a reality-warping psychic viral infection whose exact mechanisms are entirely unknown. We don't really have enough data to say that it is "realistic" or not.
 * Alternatively, it could be a case of diminishing returns or just a hard cap on how strong Evolved can be. Mercer reached the peak of power for Evolved over a year ago, Heller reached it just before the end of the game, they're on a par with each other and Heller wins through sheer determination and better close-combat skills.
 * There is no point in arguing about any of this if we can't put a decent limit on what is possible for the virus to do and how probable it is for it to advance at a particular rate, whether a certain ability comes from technology, biology, or magic there needs to be some sort of rule to let the audience know how it ticks, otherwise it comes off as an ass pull. Saying, "It's a fictional virus, it can do whatever it wants!", is a lame cop out. Mercer evolved at a fairly incredible rate over the course of 3 weeks in the first game so I don't even mind James becoming as powerful as he does, Alex proved that something like that could be done, it just seems strange that he would give up on doing the exact same thing that made him powerful the first time around. Plus aren't these Evolved entities coming directly from Mercer in the first place? How does he not have access to the collective power of the Infected if he is their Hive King? Did Mercer become lazy, complacent? Did the nuke do permanent damage? Something?
 * Alex proved that something like that could be done, it just seems strange that he would give up on doing the exact same thing that made him powerful the first time around. Once again, he didn't give up on evolving, he simply shifted his focus. He's not focused on combat, he's focused on controlling an entire army. Heller started close to Mercer's level and kept on getting more powerful by charging around, aggressively killing and eating and fighting, while Mercer focused on controlling his army and directing the Whitelight plan and Gentek/Blackwatch infiltration.
 * Plus aren't these Evolved entities coming directly from Mercer in the first place? How does he not have access to the collective power of the Infected if he is their Hive King? Because the virus does not appear to work that way. Once you create something, it evolves on its own and the only way to gain its genetic mutations is to consume it yourself. The Evolved developed their own unique mutations but Mercer couldn't access them without eating his own minions.
 * Is there an explanation or theory on how Heller did the Red Zone-wide "disinfection" after consuming the final boss?
 * Mine is that Heller became one with the Blacklight virus and sent his tentacles out to detonate the bulk of the plague like he does when he's finished with the Hunters or Juggernaughts.

Why infect Heller at all?
Is there any reason, aside from carrying the Idiot Ball, that Alex decided to infect Heller? It seems that by that time he already had most of his evolved in place. Aside from overtly screwing with Blackwatch, what could Heller really do for Alex? Seriously, giving anyone the potential powers he gave to Heller's weird; but giving them to someone who really, really wants you dead is just stupid. In addition, after giving Heller these amazing powers, does Alex closely monitor him to ensure Heller's not going to learn what he's up to? Naw, just sit back and don't do anything until after Heller eats a mad scientist you were discussing your evil plans with, no way that could possibly backfire.
 * Maybe Alex just wanted someone to succeed him in case he was somehow killed and destroyed. Second, Roland isn't exactly powerful enough to control the Evolved. So Alex just needed another second in command. Turns out,
 * It is entirely possible that Mercer figured Heller would come over to his side after Blackwatch tried to experiment on/kill him, and indeed, Heller does favor Mercer's viewpoint at first. However, he eventually turns on Mercer, and once Mercer notices that Heller is acting against him, he immediately tries to kill him.
 * Considering how were completely devoted to Mercer and his cause, maybe this is a known side-effect of the viral evolution, and Mercer was expecting it to work on Heller as well? In which case, the reason for choosing Heller is obvious - Mercer needed a Dragon, and Heller is a highly skilled melee fighter and ridiculously tough even before he gets the virus. He killed a Brawler with a combat knife while already exhausted and wounded!
 * It's simpler than that: clearly state that all but two evolved are mind controlled by Alex, and those two are herself and Heller. She also say pretty much say that making evolved is not an exact science. She got an advanced version of the "viral sonar" and isn't under Alex control, , but he has a spiked shield no one else demonstrate, that evolved girl with the whipfist etc. Whenever Alex is making an evolved, he's playing russian roulette as far as what the evolved capabilities will be, and he simply got the loaded chamber with Heller.


 * Well, Mercer did say he wanted Maya Heller partly because she "shares her father's annoyingly resistent genetics" Heller's daughter pre-prototype would not be genetically special unless Heller was somehow special even before Alex "infects" him. Maybe that is why a: he infected heller, or B: chose Maya Heller to be the spawnmother for whatever his master plan was, or C:all of the above. Which raises the question: What exactly is so special about Heller's original Human DNA?
 * Genetic resistance or something, same as any virus. He infected Heller because he was impressed, and he turned out to be a big problem.
 * Genetic Resistance? Do you mean the stubborness that makes Heller such a badass? his ability to stop mercer from Consuming him?
 * Not the stubborness, but his DNA itself. Like how some people that are infected have the genetics to become Runners, Walkers, or various other creatures, Heller had the genetics to resist the virus. It might explain why he became so powerful, but it's explained to be the reason why Mercer couldn't kill him, and why Mercer wanted Amaya.

Where's the Bloodtox?

 * Okay, Blackwatch - you have a substance that is in no way harmful to humans, is toxic to the virus and has proven to be easily distributed in both a liquid and vapor form, not to mention having had enough of it in Prototype 1 to PUMP IT INTO THE NEW YORK UNDERGROUND. Why are you not using it?!
 * Alex grew an immunity to Bloodtox in the first game and  so maybe Blackwatch already tried, but the new infected inherited the immunity?
 * Right, and keep in mind that their plan for  was largely the same; pumping large amounts of the aerosolized chemical in order to kill the infected. If it hadn't been for.
 * When did Alex gain an immunity? Not even Greene had an immunity. She had to make that huge shell around her to protect her from Bloodtox. Alex was always affected by Bloodtox, he just got rid of the dispensers. The use of Bloodtox was still a plausible route.
 * To be specific, he was growing an immunity. It's pointed out during one of the conversations with Cross/Supreme Hunter. Besides, one of the above Tropers already stated that Whitelight was created to do roughly the same thing.
 * I think the Bloodtox was originally going to be in the game but got dropped part-way through development. The concept art booklet includes a Blackwatch truck full of chemical drums, labelled "bloodtox transport".

Why are the evolved so confident?

 * This has really been bugging me. Why are all the evolved so arrogant? they all tell Heller things like "stop being such a wimp" or generally proclaiming their superiority. The best example is probably Commander Gallagher, the evolved soldier from the first mission when whitelight is mentioned. He insults heller, then runs off telling Heller how slow he is when I am never more than a foot away from him. He then hijacks a helicopter and tells me "thats the difference between you and I Heller, I can think outside of the box" That doesn't really make any sense. Gallagher is a commander. thats a fairly high rank. Therefore he would have to know that Heller destroys about 3 helicopters per failed blackwatch ambush at a rate of about 1 ambush PER HOUR. 24/7. Hell, he should know that anyway, seeing as how he is evolved himself. It just gets weirder and weirder as the game progress, since most evolved never change their arrogant attitude even though It should be obvious that Heller has been killing hundreds of their fellow evolved with all the difficulty of stepping on a bug.
 * This Troper found it hilarious that not two seconds after he said that, I jumped onto his helicopter, tore off his rocket launcher and destroyed his helicopter in under 10 seconds. If that's not thinking outside the box, I don't know what is.
 * True it makes for some hilarious CurbStompBattles, but WHY? WHY are they this stupid? any theories
 * Asking this question is like asking why mooks bother trying to fight Batman. That's just how things work.

Dr. Koenig double cross

 * When Koenig sets Heller up, he calls on Blackwatch to kill Heller. This implies that Blackwatch knows about Koenig's interactions with Heller. If that is the case, why do they allow Koenig to sick Heller on Project Orion? At the very least, even if Blackwatch doesn't know the specifics, they know that Koenig is going to contact Heller for the double cross, so they should have figured out that Koenig sicked Heller on Project Orion. What gives?
 * Heller has demonstrated, by that point, an uncanny ability to show up in exactly the wrong place at the wrong time, from Blackwatch's perspective. As far as they're concerned, it's just a thing that happens. All Koenig has to do is say that Heller stole files or ate an underling who happened to know about Orion while he hid in the closet, and provide some plausible excuse for having Mercer's number.

Evolved Loyalty

 * We know that most of the Evolved are fanatically devoted to Mercer. Is that because he controls them like he does with viral monsters, because Evolved are power hungry assholes and Mercer made them so powerful, or just because they believe in Alex's Assimilation Plot master plan?

Why Manhattan Again?

 * All things considered, why the fuck did Mercer decide to restart his plans in Manhattan? The Anchor showed him travelling the world in the year between games. If he wanted to destroy humanity, pretty much any other place in the world would be a better starting point; Beijing, Moscow, New Dehli, pretty much any city with a high population density would suffice. Granted, he had planted moles in Blackwatch and Gentek, but wouldn't it have been more simpler to go someplace outside Blackwatch's jurisdiction to start spreading the virus? Was he just so amused by the irony of restarting the infection at Penn Station he decided that overrode any pragmatic considerations?

Blackwatch causing the outrbeak

 * I don't understand why they decided to make it a lie. Rereleasing the infection as a weapons test while blaming it on Mercer as a convenient scapegoat is completely in character for Blackwatch, and it makes a hell of a lot more sense than the reveal that Mercer was lying and he really is not only evil, but evil in a way that completely contradicts his previous beliefs and attitudes and betrays his previous Character Development entirely.
 * BLACKWATCH would not release the virus they've spent decades researching and preparing to contain on a city of 12 million as a "weapons test". thats not a test. that's field deployment.