The story's ending of Crysis 2 seems like a confusion for many. Please someone explain to me whether Alcatraz dies, loses his mind or Prophet begins to control him??

If you play Crysis 3 you will know.

Anyways I'll say it
*spoiler*
His personality file stored in the suit is beyond repair(don't know if the mind is affected, maybe explained in Escalation), so the only active personality in the suit is Prophets(memories etc) which the suit assimilated into Alcatraz body or whatever
le edit Sigh apparently Alcatraz willingly gave his body to Prophet ai :/