SPOILERS WITHIN! BEWARE! YARR! I MEAN IT. SPOILERS AHEAD. THIS POST WILL RUIN THE GAME FOR YOU IF YOU READ IT. SERIOUSLY....
My first choice was the mind-meld with the AI. I then went though and beat the other two. I much preffered the ending to the AI one though. If I ever write some AI software I'm gonna nickname it Shodan or Daedalus. ^_^
"Show me an operation that is running smoothly and I'll show you someone who's covering up mistakes. Real boats rock." - Frank Herbert