yeah, I didn't make much of a deal about it at the beginning of the outline, but the player's character is actually psycotic.

The battle against your friend could even be purely metaphorical - the "evil" personality is trying to kill the "good" personality, and in the process, he forces you to kill your own friend (through appearing near him, thus meaning you shoot him). So the "good" personality destroys the "evil" personality, but at great damage to his crew and the ship. You could even have things like the "evil" personality taunting him and luring him to the main cockpit. After you find that you killed your friend, you commit suicide by jumping after him.