We got n00bs in this thread, spoiler!
Anyway, that can't be right, How could Solidus have been both the President and Raiden's adoptive father? Did Jack have amnesia or something? That can't have been right. I want to say it was the Colonel that turns out to be a malevolent computer.
Man, MGS4 could have been so much better if it didn't have to wrap up all the clownshoes mental bullshit from Sons of Liberty along with all the marginally less mental plot twists and awkward retcons from the rest of the series. They did about as well as they could, but it still ended up as a boilerplate "fuck it we'll throw EVERYTHING at 'em" anime finale.
Still bitter about how they completely fucked off Ocelot, the only consistently great thing about the series up til the Sons of Liberty point of the continuity.