Well I've been looking over the posts so far and I've had an idea, with these 'factions' within the alien race, there could be one that views that they don't have a right to abduct and experiment on the other sentient beings of the galaxy (Humans). The surviving Alien of the crash is one of this faction and after the crash hetries to stop the abominations killing the local humans. This also explains why he'd be willing to help the player. Also to explain the lag between the destruction of the other alien ship by Mothership Zeta and the Nazi's finding it, long Cryo extraction processes could be the reason, as in Mothership Zeta, People brought out of Cryo too quickly either loose their sanity or slowly lose health until they die. So, when the nazi's went into Statis, they left a computer to monitor orbital re-entries and wake them following the eventuality of an Alien incursion. When Zeta destroyed the other ship, the debris alerted the Nazi's, who beagn to be awoken... Also, somewhere in this thread, someone mentioned the possibility of Paulson and Soma still being on Zeta, however they both leave the ship after the DLC, Soma for the Capital wasteland and Paulson for God-knows-where. New Vegas Perhaps? He could join the courier at Area 51 to help-but it would take some explaining why he wouldn't attack your alien companion. Keep up the good work, and I'm willing to help in any way I can, although I will be away from a computer for the next 5 days...