He didn't randomly disappear because he was actually Solid Snake all this time. That's why he looks like him and has the same voice actor (David Hayter).
>>723966321 (OP)
Now that I think about it, MGS2 is probably the ONLY time in the series where Snake actually does real covert spy/espionage work instead of trying (and failing in every cutscene) to “sneak” into a location to do his mission.
>>723969854
He did fail all his sneaking attempts off-screen though. He got caught by Vamp as soon as he entered and would've died if Raiden didn't show up, he had his fights with ninja-Olga on the Shell, and the flashback to how the tanker mission went down shows him in a gunfight with guards.
>>723966321 (OP)
There's a fan theory that he is actually Solid Snake. But I struggle to see how that would make narrative sense. More likely to be yet another clone of BB that we just don't know about yet.