This is because people are asking through PMs the story.

1-Q:Why aren't the CELL and Marines working together to defeat the aliens? Why are they against eachother?
A: Because CELL is on a see-to-kill basis. They kill everyone, simply trying to wipe New York out and they are trying to kill Prophet since he is infected. They aren't evil, they just want to stop the alien virus. But the marines want to make sure they SAVE as many people as possible. In addition, CELL works against the Pentagon and the political leaders while the Marines work for them. Why does CELL work against Pentagon? Because Jack Hargreave sees them as corruptive (remember, the guy's insane).

2-Q:What's Gould's purpose? Why does he hate Hargreave?
A:Gould just wants to cure the virus and save New York by helping Prophet. Early in the game we collect tissue samples from aliens so he can study them. He wants to get a vaccination. He hates Hargreave because Hargreave is essentially the "BIG BOSS" at CELL and is crazy. He wants to kill the aliens using the nanosuit 2 but as we see, Prophet was angry at Hargreave and essentially basically told Gould all about him.

3-Q:Why did Prophet go work for Hargreave? Why did he take the nanosuit 2? Why did he work with Gould?
A: Prophet worked with Gould in an attempt to get a vaccination set and done. Also it was because CELL eventually wanted to kill him because he was infected. Prophet worked with Hargreave after the Lingshan incident because he really had no choice. Nanosuit 1 was a test run, the nanosuit 2 is basically the TRUE suit to make the weapon against the aliens. It had a stronger symbiosis and alien integration to work against aliens. What you did as Alcatraz when Hargreave commanded you was what Prophet was supposed to do.

4-Q: Why was CELL trying to kill Prophet? Why didn't Hargreave stop CELL from this?
A: Because Prophet was contaminated and had the nanosuit 2.0. Hargreave wanted the suit and was ensured by Lockhart that he'll get the suit but Prophet dies. Hargreave is okay with this because he wants to go INTO the suit and he wants to collect the spores and create antispores and kill the Ceph BY HIMSELF. He thinks he's the only capable human of doing it.

5-Q: So, if Hargreave wanted to get the spores himself, why did he let Alcatraz do it? He wasn't going to let Prophet do it and was going to let him die.
A: Prophet worked with Gould and probably once he got the vaccination, he'd go use the suit to kill the Ceph and then he'd go after Hargreave and CELL for the terrible things they did by lying. Prophet either way did NOT have Hargreave's trust. Alcatraz on the other hand is some new guy, so gaining trust from this person was easy. That's why Hargreave mentioned Gould said bad things about him but to not mind them when he communicates with Alcatraz. It'd be easier to just prep the suit through Alcatraz, trick him with an EMP blast and then take the suit for himself. Tricking Prophet would not be easy, and prepping the suit through Prophet would not have worked because Prophet would have stuck with Gould the whole time. If he was in Alcatraz's situation where Alcatraz and Gould got separated, Prophet would run BACK to find Gould, NOT work with Hargreave.

6-Q: Does Hargreave support humans or aliens?
A: This is rather a hard one because Hargreave, before he goes laughing insanely letting the aliens try to kill Alcatraz, he states how they are the true inhabitors of earth and how the human race is pathetic. BUT, Hargreave supports humans ultimately. He didn't warn anyone about the invasion because, again, he thinks he's the ONLY one capable of stopping the ceph. He sees humans as weak and kind of like a joke, except for him. He sees the Ceph superior and that they may as well kill the weak little humans. BUT to him, he still wants to protect humanity by killing the Ceph, it's just if humans died, it's understandable to him since the Ceph were on Earth first. He has a really high ego.

7-Q: Why does Alcatraz call himself Prophet in the end of the game?
A: From the time Prophet put Alcatraz in the suit, Alcatraz was essentially dead. The only thing keeping him alive was the suit and it's life support systems. Alcatraz IS VERY CLOSE to being dead. In addition, the symbiosis with Prophet to the suit was too strong....Prophet's conciseness was still in the suit. When the suit became symbiotic with Alcatraz, Prophet's consciousness got into Alcatraz's brain and they basically had both their minds become as "one."

8-Q: Why did Prophet kill himself?
A: He wanted to break the symbiotic link to the suit. He knew the suit was the weapon against the aliens and had it but the symbiosis got into him. He hated the link because it basically binded the user to the suit and the suit absorbed alien contents; in addition, the symbiosis was potentially fatal (Hargreave states it as a "necessary sacrafice" for a soldier; plus Prophet got badly infected through the symbiosis when he was infused with alien tissue; he would eventually get so infected due to symbiosis that he'd probably DIE...of course he'd die after walking out the suit. He'd have to be REALLY REALLY DEAD for him to die in the suit). So essentially, people in nanosuits were becoming part alien for every alien they killed. In an attempt to break the link, Prophet killed himself, hoping that at least the conciousness would break from the suit. But it didn't. He also killed himself because he was infected and was actually SPREADING the virus.
Why isn't the infection in the suit? It is, but it's now PART of the nanosuit. Not like an infection to work against though.

9-Q:What happened to Nomad, Physco, and Helena?
A: Prophet was the ONLY member left alive in his squad. He was sent by Hargreave with the new nanosuit to go test out the technology on Lingshan islands. Hargreave knew about aliens on the island, Prophet thought it was just a top secret locate and evacuate against Koreans mission and that the nanosuits would enhance combat. Wrong, they were meant to make contact with aliens in order to perform the symbiosis and for Hargreave to see what they are like now. Considering Prophet was the only one left alive, Nomad and Physco either died or went insane from symbiosis or they went back to the island to get Prophet and died doing it. Helena....idk. I assume either she went back to CIA, retired, or went with Physco and Nomad and died as well.

Okay, this should explain a lot. Story was great but it did SEEM to have plot holes. There aren't any plot holes it's just Hargreave talks more complicated with strong vocabulary and anologies and not much is super explained. Let me know in this thread if you guys still got questions. I might have messed up here or there because the story is more complex than it seems. Let me know if you manage to catch any potential mistakes, TY.

Nice post!

Thanks man, it's a refresher to the usual hate threads around here and gives an explanation to many things people didn't understand.

Why are the aliens red?

i think Q & A #9 was crap.

and #4 is wrong. The reason they were trying to kill prophet was because of that one guy demanding him dead. He was supposed to be captured alive.

These are only YOUR assumptions. The story itself has many plotholes, now whether they intentionally left them for people to create their own versions of things i have no idea, but it doesn't have to mean your point of view is canon.

There are plot holes in the plot holes!
That is called "Swiss cheese"!

Okay, now explain this - what in the heck is the "human tissue" goop Alcatraz finds when he's looking for Ceph tissue samples and what's going on there?

Well theres actually an explanation for that in game. The "goop" is just how the Ceph dispose of the human bodies.....by breaking them down

Well theres actually an explanation for that in game. The "goop" is just how the Ceph dispose of the human bodies.....by breaking them down

Really? When does that come up? Funny timing, actually, because I just played through the section again where Hargreave's talking about BSE and disposing of carcasses after mass slaughter, but I don't remember him saying anything about the, uh, "goop". So either I'm deaf or it's explained somewhere else and I missed it...

Well theres actually an explanation for that in game. The "goop" is just how the Ceph dispose of the human bodies.....by breaking them down

Really? When does that come up? Funny timing, actually, because I just played through the section again where Hargreave's talking about BSE and disposing of carcasses after mass slaughter, but I don't remember him saying anything about the, uh, "goop". So either I'm deaf or it's explained somewhere else and I missed it...

It was said, Gould said it and it was before the middle of the story. Turn on subtitles, you pay more attention to detail that way.

Why are the aliens red?

i think Q & A #9 was crap.

and #4 is wrong. The reason they were trying to kill prophet was because of that one guy demanding him dead. He was supposed to be captured alive.

Lockheart with the CELL board wanted Prophet dead. But Hargreave didn't care. Strickland wanted Prophet alive, and we all know why. Hargreave simply wanted the suit.

And whether Q & A #9 was crap or not, it's basically what happened. Prophet was the only one left alive in his squad. Nomad and Psycho both are dead, or so it is said.

Also, the aliens are red due to evolution. You can say it's also due to no more ice effect as usual, but it's simply evolution.

These are only YOUR assumptions. The story itself has many plotholes, now whether they intentionally left them for people to create their own versions of things i have no idea, but it doesn't have to mean your point of view is canon.

Not really man. It's not assumptions, it's me playing Crysis 1 and Warhead too many times to count and playing Crysis 2 MULTIPLE TIMES (60+ hours logged into SP a bit too much? Idk lol). You need to pay close attention to EVERY word in the story and every element. Make as much connections as you can. There are no plotholes except for maybe what Nomad and Psycho did after they left the island. Did they go back? Were they captured and killed by CELL? Who knows. THAT is the only plothole I can think of.

The story could have used so better explanations in Crysis 2, but there are no plotholes really. Play again, multiple times, you'll see it. And try to make out what Hargreave says, he speaks with specific tones, uses strong vocabulary (stronger than the average vocab. people use), and literature devices.

This is a good thread, A+ thread... For real.

Link the Ceph's insect like machines sticking needles into corpses like Mosquitos, Hargreaves statement when viewing this operation on a pile of human..."remains", and then the flying machine's cargo and it is logical that this is what the Ceph does. For what purpose that they transport it places i don't know, but thats the point, leaving the answer in a possible third game.

Hey man, really cool explanation. My first play through of SP was on post human warrior so I was having a hard time listening to all the dialog, I was just trying not to die, haha. I do have one question though, what was the Lingshan accident?

Still no explanation on why the aliens sent a broadcast out to space then started to popping out from underground. Not a plothole, but just a whole bunch of unexplained story elements that doesn't easily fit with Crysis 1 stuff.

Sure you can add in extra sources to make sense of it all, but that just shows how weak the two stories connect. Only detail from first Crysis that works into Crysis 2 is that Prophet have nano suit, there are aliens and Strickland died (the purpose of Tara Strickland character isn't that well explained in the actual story telling of Crysis 2 either lol). Outside of that there are hardly any connections.

Still no explanation on why the aliens sent a broadcast out to space then started to popping out from underground. Not a plothole, but just a whole bunch of unexplained story elements that doesn't easily fit with Crysis 1 stuff.

Sure you can add in extra sources to make sense of it all, but that just shows how weak the two stories connect. Only detail from first Crysis that works into Crysis 2 is that Prophet have nano suit, there are aliens and Strickland died (the purpose of Tara Strickland character isn't that well explained in the actual story telling of Crysis 2 either lol). Outside of that there are hardly any connections.

They sent a broadcast/signal out. It was Helena who just had a theory that it went to space. We don't know for sure. For all we know, the signal was to wake the other Ceph up.

I never added extra sources to make sense of it all. You just need to pay attention and make the connections. The plotholes "supposedly" existing, do not exist. Crysis 1 and 2 connects well enough. Crysis 1 is rather considered the Linshan incident in general terms to Crysis 2. That's the meat of it. In terms of getting into detail, then they don't connect AS WELL unless you actually pay closer attention. Regardless, I have shown there are no plotholes.