Something brought up in the podcast was the possibility that the ship wasn't previously ever alive and only had the mission because that's what the ship's computers were devoted to at the time. Because Dark Energon brought one of Ratchet's tools to life in a previous episode. One thing I don't think has been mentioned before and I'm not sure why I didn't even think of it till now. They got the Nemesis flying again because they used Dark Energon and then they regained control of the ship by ejecting the Dark Energon from the power core or whatever so shouldn't the ship have crashed again because that was only thing keeping it in the air? This wasn't in the podcast but something I just thought of and am now kicking myself in the butt so to speak for not thinking of it sooner.