Comes out of retirement in the next MGS game (after MGSV)?
On one hand you'd have an extremely retarded decision that spits in the face of MGS lore, and on the other you could have one of the best character returns of all time.
The explanation?
NANOMACHINES SON
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Nanomachines? One final mission...again? That'd just be silly. I would prefer to see an interquel between MGS1 and 2, and it'd be about Snake and Otacon's early activities as a part of Philanthropy.