I seem to remember that at the end of the game, playing as Ian, you get to make a choice of what final mission to take. One good choice, where you save your allies and friends, and one bad choice where you sacrifice everyone for victory. Both lead to different endings.
Black night takes over from the bad ending, as such it's a kind of "alternative history" game, like the mirror universe in Star Trek. :) Ian is evil, he let his sister die in order to win, Jen left when she found out what kind of monster he has become etc...
Been a while since I played the games though, so I can't quite remember if it's true.