As i've said, I don't think even CryTek know WTF the story is meant to be in this game 
SPOILORZ
Though really, basically, Prophet said the nanosuit developed a symbiotic relationship with him. When he killed himself he wanted to break the link, but it turns out his consciousness was still alive inside the suit. Basically he was the suit from that point forward, guiding you all the time. Alcatraz was heavily wounded, and was a 'dead man walkin'. The suit fused with his body, repaired it, as explained by the medical scanner. In the end Prophet and Alcatraz became one - Alcatraz absorbed Prophet's memory and personality as it was stored in the suit.
Yes it's dumb.

SPOILORZ
Though really, basically, Prophet said the nanosuit developed a symbiotic relationship with him. When he killed himself he wanted to break the link, but it turns out his consciousness was still alive inside the suit. Basically he was the suit from that point forward, guiding you all the time. Alcatraz was heavily wounded, and was a 'dead man walkin'. The suit fused with his body, repaired it, as explained by the medical scanner. In the end Prophet and Alcatraz became one - Alcatraz absorbed Prophet's memory and personality as it was stored in the suit.
Yes it's dumb.
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