@GamerKid303 have you used any cheat codes with this game? Or did you try to jump the storyline?
You probably used a bad code, which flipped the flag for Drayden.
Drayden threw out and withdrew his Haxorus, despite NPC character not displayed on screen.
(that's probably a symptom of the issue)
If anyone else has a save that's around the same playthrough, I can use their flags, stitch it into your save, and salvage your save.
edit 1: My restoration plan is going well.
edit 2: Save salvaged! Use this save! test4.sav
For those interested in how I did it: