Someone posted a thread in the forums basically saying they had beaten Crysis 2 but wanted some clarification on the storyline in the game. I made a brief synopsis answering most of the questions I saw people posting in the thread, but when I clicked to "Post", the thread had been locked. I'm just posting it as a blog so anyone who's interested can check out my take on the Crysis 2 story. This is what I was going to post in the thread, verbatim:

I do believe that Crysis 2 actually has a very good story underneath, but the way it was presented to the player was done very poorly. At first I thought it's because I hadn't played Crysis 1, but a friend of mine that's beat Crysis 1 explained to me the story in Crysis 1 and it has very little to do with Crysis 2. They simply didn't do a good job of explaining what's going on. You have to really basically try and deduce who everyone is, what they want, and why they're doing what they're doing. However, I've tried to piece together a brief synopsis of what happens in the game.

WARNING, THESE ARE MAJOR PLOT SPOILERS!!!!

What I got from it is this: The game starts off with Marines being sent to assist with an alien invasion in Manhattan. You're one of them and your name is Alcatraz. Apart from physically invading Earth with a military force, the alien Ceph are also building spires which release a deadly Spore virus into the air. This is basically the perfect one-two combo for colonization. Apparently, Prophet is somehow infected by the spore virus himself, although the game does not say how. Maybe someone who played Crysis 1 could answer that, I don't know. Anyway, he kill himselfs. You find out later that the suit is symbiotic (during one of his flashbacks showing when him and Hargreave have a serious argument and falling out) and it appears that he kills himself as he feels he is no longer fit to fight the war against the Cephs due to his illness and the suit will reject a new wearer unless the former wearer is dead. Somehow Dr. Nathan Gould detects that Alcatraz's new suit is reacting with the spore virus in its deeper layers.

After Gould is captured while trying to get a deep layer scan on the suit, Hargreave takes over as your "guide", so to speak, and you're running around Manhattan trying not only to stop the invasion but also caught in a power struggle between Hargreave and Lockhart within C.E.L.L. Lockhart is sending wave after wave of C.E.L.L. troops to kill Alcatraz because he believes Alcatraz is a biohazard (he thinks he's Prophet) and because of a moral gripe with the Nanosuit, which we learn more about later.

It becomes clear later at this point that the reaction in the deep layers of the suit is the Nanosuit re-engineering the spore virus to make it harmless to humans and instantly deadly to the Ceph, using their own weapon against them. Hargreave reverse-engineered the suit over decades from Ceph technology which I guess explains how the suit can do this. After helping with a couple of evacuations, the suit has completed the Ceph-killer spore, so Alcatraz enters one of the spires. Reacting with the spire, the suit kills all of the Ceph as well as the original spore virus in the area. Later you catch up with Lockhart and kill him.

After this, Hargreave betrays you, and tries to keep the suit. The suit rejects removal because it's assimilated to Alcatraz, and you are freed from captivity by Strickland, who reveals she's an undercover CIA agent assigned to C.E.L.L. by the U.S. government, and SHE was the one who ordered Marines deployed to assist Prophet, basically kicking the game's plot off.

This next part is a little murky, but I what I did get from it is Hargreave's been in cryogenic stasis for years now and everything he's done since then has been his consciousness communicating with the outside world via computer tech. It appears he wants to take the suit for himself, perhaps because the suit will restore his health (we never find out why he's cryogenically frozen) or perhaps because he simply does not trust Alcatraz. But I do believe he specifically says he had hoped to wear the suit himself.Hargreave gives Alcatraz one more upgrade injection, but to be honest I couldn't possibly tell you what the injection does as there is no explanation or change in the way the suit works or handles. Your guess is as good as mine. At this point, and for reasons which we can only guess at, Hargreave decides to commit suicide by blowing up the entire facility he's in. This makes very little logical sense in the narrative but made for a very exciting section in the game so I guess that's why they had him do that (similar to how producers of Hollywood action movies require an action scene every x number of pages in a script).

So then after that you basically go to the heart of the Cephs' Manhattan invasion, Central Park. Alcatraz mingles with all of the spires in Central Park, including the main tower, causing one huge reaction which kills all of the Ceph in the city as well as the spore virus. Then, Prophet's consciousness begins to speak to Alcatraz via the suit. It appears his mind, or part of it, has somehow been saved in the Nanosuit's memory. It is unclear though, whether Prophet is merely communicating with Alcatraz via the suit a la Cortana in theHalo series, or if Prophet has somehow taken complete control of Alcatraz. If so, what happens to Alcatraz's consciousness? The game ends abruptly with Alcatraz saying "They call me... Prophet," and it's Prophet's voice actor that reads the line, so really it's quite hard to say exactly what happened there. Needless to say, I think the dev/writing team could've done a much better job of making the story clearer. It's like they have this vast, intricate story of the Crysis universe but they just don't seem to know how to present it properly.

Anyway, that's my take. Sorry for the wall of text, I just tried to answer all the questions I saw in the posts above me.