In Crysis 2 we see Prophet suicide shortly after he rescues Alcatraz, but in Crysis 3 Prophet makes a return to seek revenge. Can anyone explain how Prophet is well and alive in Crysis 3? almost 20 something years after Crysis 2.

This has been discussed to death. Read the freaking book. Hell, just watch the ending to Crysis 2.

SPOILORZ (yeah, right...)

Prophet is alive inside the freaking NanoSuit's AI and is part of it (if not all of it by now).