After reading http://secure.gamesas.com/forums/viewtopic.php?f=58&t=61186 I am a little disgusted at how complicated the lot of you are making the story out to be. It's not the easiest story to follow but it's not the hardest either. So, if you're looking for answers you've come to the right thread. Without further ado, let's start with Crysis 2 since Crysis 1 doesn't have much impact on the story. Feel free to dispute anything AFTER reading ALL of this. Also as a disclaimer: nothing here is regarding the books or comics because the games (mainly crysis 3) have argued with points in the book.

So, the first thing that happens is the Force Recon submarine is hit by Ceph gunfire. Every Force Recon marine escapes, except that Chino is missing. As they talk, they are hit by more gunfire. Laurence Barnes shows up with a HMG (if I remember correctly), and fires at the Ceph gunship. Once it is no longer a threat he finds Alcatraz floating in and out of consciousness. It is here we learn Alcatraz is the sole survivor (besides Chino) of the attack when Laurence states,"**** Ceph wiped you all out?!". He drags a heavily injured Alcatraz into a room. It is here Laurence removes his Nanosuit, which reveals a black under-suit that prevented the Nanosuit from fusing with its host the same way it later does with Alcatraz.

When Alcatraz later wakes up in the Nanosuit, it plays Laurence's last message. This reveals Laurence shot himself after putting Alcatraz in the Nanosuit, the sole thing keeping him ALIVE. Laurence stated he had to "break the link" by killing himself, and while his link with the suit was broken the Nanosuit had already created and stored a personality file on him. Anyone who complains about how unrealistic this is: first this is a game. Second its possible because SECOND (the non-SENTIENT suit AI) is symbiotic and in this case is and was literally inside Laurence's mind. SECOND made Laurence smarter, but at the same time was recording his speech patterns, personality, memories, experiences. Everything that defined Laurence was stored inside the suit.

At this point in time, SECOND also started storing everything that defined Alcatraz. So, as a lot of you used to prior to Crysis 3. It was one body, two minds. Alcatraz wasn't dead in any sense. When Gould and Alcatraz make it to the CELL lab on Wall Street (again, if I remember correctly) the scientist says Alcatraz has multiple broken ribs, damaged lungs, heart, brain trauma. Without the Nanosuit, yes Alcatraz WOULD be dead. But as Laurence would say, he's a dead man walking. Due to the amazing Nanosuit, Alcatraz is perfectly fine.

The first time Alcatraz tries to repurpose the spore, he learns the suit can't interface with the spore. But after he kills the Ceph (stalker?) the Nanosuit starts reacting to the Nanocatalyst. This is when Alcatraz's personality file within the Nanosuit starts to get corrupted. After each successful repurposing of the spore the file got more corrupted.

Because the Nanosuit had stored a personality file on Laurence, Alcatraz was able to have flashbacks of events that Laurence had experienced. Sooner rather than later Alcatraz was experiencing the recreation of Laurence. Alcatraz was able to hear Laurence's voice when he did certain things, like at the end when he hears Laurence saying, "Come on Marine, finish what I started". After this event, Alcatraz is knocked unconscious and because he is technically dead the Nanosuit has been using his personality file from the moment he got the Nanosuit. At this point the file is 42% corrupted, enough that the file is placed into indefinite storage.

So what happened once Alcatraz "disappeared" from existence, or as a lot of you seem to think died? The Nanosuit retrieved Laurence's file from storage and used it instead. While all of this was happening we see and hear Laurence speaking. He says,"thought I'd gone, marine?". This is the Nanosuit TELLING you (though subliminally) that it is retrieving Laurence's file. The Nanosuit switched profiles. Think of it as the Nanosuit being able to contain multiple profiles, but allowing only 1 to be active at any given time.

So Prophet wakes up, and climbs out of the rubble. Maybe you've noticed this is the first time I've used the word Prophet. That's because Prophet isn't just Laurence Barnes anymore. Prophet is the ultimate war machine. Prophet is Alcatraz as well as Laurence Barnes. To quote another user, "Prophet is predominately Laurence", for reasons I've stated above but he is not just Laurence. He is also Alcatraz.

(Another disclaimer: A lot of this part comes from the Crysis 3 wikia, which I assume was found in the new book.)
Which brings us to Crysis 3. The number one question is what happened in the 24 years between Crysis 2 and 3. After Prophet "awakens", he goes on a hunt for the Alpha Ceph with Pyscho. They end up in Seberia where CELL takes Prophet down with K-Volts. He is imprisoned for a long time. (So far there is no info on how long he searched for the Alpha Ceph, or how long he was imprisoned).

Skipping ahead a bit, when Psycho and Prophet are in the lab Psycho and Claire unlock the safety measures on the Nanosuit. What this does is allow the Nanosuit to take on any shape or form. Claire freaks out because Prophet is already under Ceph influence. The Alpha Ceph has contacted Prophet and shown him visions of the future. He has Ceph DNA in the suit. Prophet isn't just Laurence Barnes, or Alcatraz. Prophet is now part Ceph. To quote Claire, Prophet "could literally turn into Ceph" now.

They also find out it was Claire that removed Psycho's nanosuit through a process called "skinning", but this is more about Prophet so moving on. At the end when Prophet wakes up in a house presumably in Lingshan it looks as though he has his own body back. Which confuses a lot of players into thinking Laurence Barnes is still "alive". No, Prophet is still (in) the Nanosuit. Now, though the suit has taken the form and appearance of his body. That's why you can see Armor mode "scales" on the side of his face, as well as why he can cloak "without the suit" at the end.

To end this all, no it's not actually Prophet impersonating Psycho in the CELL facility. It's actually Psycho.

Added spoilers to the title

you might wanna add a spoiler tag to this thread for people who have not finished the game yet

There is a difference between a complex story and a poor mess of a story trying to appear viable

When your story is so bad,that your second game is an almost different franchise than the first,and there is almost no link between any of the elements of the two games,and you constantly make up new facts out of nowhere to try and fix this,and you include half a game worth of story in a comic which most people wont' even find,and you even make a whole 3rd game to convince people that this was what the story was supposed to be,with another set of instantly made up facts,and half your plot holes have excuses in the form of data pads...

..then you know that you should fire your storywriter,and get someone who can actually do his job

The problem with the next game if you fire the storywriter is that it will be even worse, at least the game wouldn't change again, I wish we could see what the possible plot was from Richard Morgan and the guy who wrote Crysis..

I've been wondering the exact same for a while. I think we would have saw a little more personality/background on Alcatraz if it were the case. I still love Crysis 3 though, just wish they could have stuck with one writer for the series.

Good post Elitis, I was always wonder wtf Prophet was wearing in the beginning of Crysis 2 lol. I think we need story DLC that bridges the 20+ year gap between Crysis 2 and 3. As well as DLC that brings a conclusion to Nomad, unless something else is planned for him in the future. At that point I think the Crysis story involving Prophet and the rest of the characters can come to a full closure.