Ok, so the last i saw, was in crysis 2, Prophet shot himself in the head and gave up his suit. Now in crysis 3 your prophet again and he is alive? im confused...

Basically, the suit had Prophet's mind stored. And since Alcatraz didn't have the protection suit that goes between the nanosuit and the human body, the suit has grown into him. By the end of C2, the suit replaces Alcatraz's mind with Prophet's, or at least that's what I understood.