I'm not familiar with the plot of the game, but consider this: is it possible that the reason why Mega Man no longer exists in the Mega Man X era because of the events of Mega Man II?

Basically, the reason why Mega Man isn't there is because he was turned into Quint, and subsequently destroyed by Mega Man?

Yeah, because I doubt Mega Man would have been just left laying there for Wily to reprogram unless Dr. Light and the other characters had already died/shut down. The time that Wily traveled to could very well be the same time that Dr. Light had already passed on and X was still under stasis within his capsule.

Shit, what if instead, Wily finds X, reprograms him, and brings him back to the present of the Classic timeline to fight Mega Man?

That would suck.

Thank god X was stuck under a rock.

Even still, if this happens to be the case, its a rather depressing end to Mega Man's story.

Fridge Horror a go go, baby.

I think it's more likely that after light passed away, megaman, roll, auto, eddie, Rush, and all the others just broke down.. It's possible that auto survived the longest and kept everyone going for a little while, but he wasnt light, and didnt have the same talents..

Since Light was the only one that could really keep their maintenance in good shape, his death would mean they likely went without repair for too long, and just broke.. Not exciting, but it flows with the story better.

Protoman had a faulty generator, and his days were numbered from the get-go. He was likely the first to go.

As for Bass, I think Wily finally had enough and destroyed him.

They probably all ended up in a robot museum, along with all the other robots.

For serious, Bob and George gave us a animated reason of the end of the original.

Zero is unleashed, kills everyone save for Auto and Protoman, and is put away.

It's worth pointing out that in Battle Network, Wily is still alive and Light isn't. If Wily outlived Light in the mainstream universe as well, and the doctors didn't have kids like they did in the Battle Network world, then Wily could quite easily have captured a deactivated Mega, and destroyed the others without resistance.

Rockman Shadow was a copy of Mega Man built by Wily, but the idea was scrapped in favor of making Mega Man into Quint. Ergo, Mega Man did not become Mega Man Shadow.

That've caused a time paradox anyway.

The idea Hollow's getting at is that Omega was essentially what Zero was meant to be, had his programming not been altered.