"Mega Man and X travel back in time to find a way to fix the future."
Mega Man and X are in the past, complete with 8-Bit format. Dr. Light comes in and freaks out at two Mega Men, but he forgets that and exclaims that Dr. Wily escaped from jail. Since he didn't say Wily escaped again, X deduces that they are right before the second game.
The storyline takes a small break for the first Bob and George birthday party.