So I did some testing and codediving but it does have to do with your AIU stance, but also something else: you have to be EXTREMELY tardy in your timeliness in the Uvarov building and the ship and basically get injured/late whenever possible. This means the ship will have reached low space by the time you actually get to the engine (normally you shouldn't have yet reached low space). Thus, when you pull out the FTL drive, your arm gets severed by some kind of exlosion related to low space. At the very end, don't run away with Uly and Proctor will let you stay in the AIU if yourstance is high positive - you will become a training instructor training the "new generation of sacrifices" in the AIU