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I honestly think he was tipped by the patriots to show up without GW knowing. I think the reason why this happened was because the patriots wanted to see if GW could even work it's way around this unforeseen variable and still solve the crisis that it was presented with. It would also explain the mysterious contributor on the list of patriots that Otacon mentioned at the end of the game, although I don't know how it would have tied in with them being dead for 100 years (pseudonym's perhaps?)
But then MGS4 came along and retconned the whole thing.
"I loved being in the boy scouts. We went to 'Nam." - Rich Hall