For Crysis fans who have only played Crysis 2 and have seen the new E3 trailer/gameplay for Crysis 3 may have been confused of why Prophet is back, after killing himself in the previous game. Also their has been lots of speculations on Crysis 3 forums of who you will be playing. I want to lay it straight out to everyone that you will be playing with Prophet's mind set but in Alcatraz's body. The Nano Suit was able to take/copy a peace or all of Prophets mind while he was wearing it and store it into deep the suit's layer tissue. I don't know if any of you are marvel fans but the nano suite is like the helmet of fate, it needs a host body to be used. After the wearer or host is all used up the host mind is stored away, then a new host body is needed. Alcatraz was the new host and now the suit is infused with his body there is now taking it off, until his body dies. If you remember at the end of Crysis 2 when Alcatraz releases the cure to the Spore in the Ceph Tower several days later he awakens from being knocked out after the blast. But it was not Alcatraz's mind who awoken it was Prophets mind. This is what I think, Alcatraz's mind was left unconscious after the blast and the Prophet's mind toked over.
There could be conflicting issues in Crysis 3 on whether who has control over the body, Alcatraz or Prophet, later on in the game but you do start off with Prophet in control.