Near the end of 'This Galaxy Ain't Big Enough..' page: http://fallout.wikia.com/wiki/This_Galaxy_Ain%27t_Big_Enough...

Quest stage number 60, just tells the player that there is an option to set the alien ship to self-destruct. There is no information that I could find on the net to back this up. I found no device that does this on the ship that I could find during the game.