I once read a very well written X series Fanfiction, (what a rarity those are...) That had it that after Wily was defeated for the last time, his robot masters were overwhelmed and were beaten, and crucified in a hidden valley far from the city or something X and Zero find it by Accident, and they encounter Vile there, who tells them about it. He learned about the placed because Sigma is obsessed with everything Wily. He then asks them about the museum displays. how there's a broken Bass on display. X mentions that he thought it was all replicated, and Vile tells him its not, That the bass there is real. "Right down to the Japan flag pole through his chest" Treble was apparently dismanteled and sold as spare parts... I dont remember what happened to Megaman though. However, a few of the robot masters are actually still alive. they are all horribly maimed and crippled,having been there for that long, and I think one or two are crazy from the pain. So X Zero and Vile temporarily set aside their alignment to put the still living masters out of their misery.
It was interesting.