Ok was stuck on this and I think have kind of worked it out From what I can tell your not supposed to be able to kill any of the bosses but the last one however something has gone wrong and they die when they are not supposed to the trigger for being pulled back is supposed to be some sort of move the boss does but you can kill them before your supposed to easily and since the boss is dead it cant perform the action to move the mission along its not a fix but try using a gun with more spread out damage like a submachine gun or an auto rifle or any of the small but many bullet guns and just get the boss to low health instead of killing it and wait for it to do some special thing then it should take you back to the pyramid properly