spoilers following, even though that is obvious by thread title...
I believe the new foxdie that Drebin injected is killing off the mutating old foxdie that was to cause him to become a WMD. I believe Otacon or Naomi said that there is no guarantee that the new foxdie won't eventually also mutate.
Like most of the game, it parallels MGS1. Basically, Snake is being told he can live, just like the end of MGS1. The difference is that the aging due to being cloned doesn't give him more than a year...or was it 6 months...whichever.
The solution could easily be a process to reverse aging due to cloning, but Kojima has said that a future MGS would not star Solid Snake, and that's the way it should be after that game and how it ended.
The only thing that upset me was Meryl ending up with Johny, but that is pretty ironic.
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