Obviously this is my own fault for messing with the debug, but I followed the guide on what to change in order to get the 'good' ending of the game - which involves changing to not having fought Taka at the sewers. I'm currently in the postgame and my 'mons are around lv115, but when I headed to the desert via train I was met with Taka and let him go with me, my first mistake.
As I've already done the train puzzle, I can't seem to find another train to get me to the scrapyard. I also can't fly out of the situation to escape it. Am I just stuck in the desert now?