This article was made for easy and quick access to the fates of the characters.
Mega Man-After recovering from the fall and Mega Hulk, Dr Light ran a repair progress, which extracted Vic. He was in several more linear video games. Killed in Cataclysm.
Proto Man-After training, he was out of town when the Cataclysm hit. He then changed his name and appearance to Prometheus. He would blame himself for everyone's deaths.
The Author-He stopped running the comic. This meant that he refused to intervene in the Cataclysm. He would change himself into the Shadowy Author and travel back in time to warn his past self about the Cataclysm.
George-Got a job in the real world. He could still be a superhero, but the work was boring. It did pay the bills. He always wanted to visit the Megaman Universe, but real life intervened. He never got another chance to visit.
Bob-Became the CEO of a computer company which made it into the Fortune 500. His software defeated Windows and Bob made trillons. He never gave up his plans to be a supervillain and died during a battle with Delta Flight.
Dr. Light-Returned to his lab to work on robotics like sentient holograms which could continue his work long after his death. His alcoholism spiralled out of control. He would have died had the Cossacks not invented the artificial liver. Killed in Cataclysm.
Roll-Retired from fighting crime and returned to old job as Dr. Light's maid. She came to hate her life and eventually planned to feed Dr Light to crocodiles. The blood of the dead had no effect on old Light. Killed in Cataclysm.
Dr. Wily-Returned to his lab and attempted to take over the world several more times. He was the first to be killed in the Cataclysm, after activating Zero early.
Bass-Recovered from the fall and went back to Wily's lab. He then went throught several more videogames as the anti-hero. His secret love for Roll was never discovered or further addressed. Killed in Cataclysm.
Mega Man X-Present X continued to sleep in his capsule until Dr. Cain wakes him up later. Future X went on for several more games and then sacrificed his body to defeat a Dark Elf. He became a spirit-elf.
Zero-Present Zero was activated and killed off every remaining character* until defeated by Auto. He was buried by Proto Man in a mine shaft, uncovered a century later and defeated by Sigma, and then reprogrammed by Dr. Cain. Future Zero returned to the future and died a few more times. He then sealed himself off in a capsule and awoke a half-century later. Nothing else is given.
Ran-Returned to the Cossack labs, was caught in a temporal accident and frozen for a century. His regenerator made an evil copy. Ran was eventually unfrozen by Plague.
Nate-Died when his corn syrup hardened, activating a system shutdown.
Chadling-Ballooned up to 2000 pounds and died from his own obesity.
Mike-Got to Ninja Ned's training dojo with him. He died in an maneuvre biting his own tongue off and bleeding to death.
The two Mynd's-Stopped duelling with the conclusion that they were equal skilled. They then travelled to a dimension where it's legal and married each other.