Characters on Mega Man's side:
Nick Fury, Mega Man, Darci Roll, Supergirl, Wolverine, Storm, Shadowcat, Rogue, Professor X, Ice Guy, Phoenix/Jean Grey, Beast, Cyclops, Angel, Nightcrawler, Mr. Fantastic, Invisible Woman, The Thing, Human Torch, Spider Man, Iron Man, War Machine, Cyborg, Captain America, Batman, Black Canary, Robin, Black Widow and Hawkeye
Neutral:
Callisto, Deadpool, Harley Quinn, Lex Luthor and Mercy Graves
Characters on Wily's side:
Dr Wily, Proto Man, Metal Man, Air Man, Heat Man, Flash Man, Bubble Man, Wood Man, Crash Man, Quick Man, Pyro, Magneto, Lady Deathstrike, Dr. Doom, Electro, Green Goblin, Dr. Octopus and Bane
Mega Man 2 Part 1 (4th Sep 2059) (About a year after Wily's defeat in the last part of Mega Man 1)
Nearly a year after Wily's defeat in the last part of Mega Man 1, he returns with Proto Man, those supervillains (who superheroes previously confronted) and his eight new robot masters; Metal Man, Air Man, Heat Man, Flash Man, Bubble Man, Wood Man, Crash Man and Quick Man. They attacks the city named "Metropolis" (same city those villains attacked three times in the past). Mega Man along with other superheroes returns to defeat those robots and villains.
War Machine defeats Bubble Man
Mega Man defeats Metal Man
Ice Guy defeats Heat Man
Invisible Woman and Ice Guy defeats Flash Man
Iron Man and Angel defeats Air Man, then also defeating Crash Man
Black Canary and Mr. Fantastic defeats Wood Man
Captain America defeats Quick Man.
After defeating those robot masters, those supervillains such as Pyro, Magneto, Lady Deathstrike, Dr. Doom, Electro, Green Goblin, Dr. Octopus and Bane comes to confront those superheroes.
Batman and Black Widow defeats Bane
Spider-Man defeats Dr. Octopus
Robin defeats Electro
Angel defeats Green Goblin
Wolverine defeats Lady Deathstrike
Ice Guy defeats Pyro
Invisible Woman and Cyclops defeats Dr. Doom
Supergirl and Mega Man defeats Magneto.
Then Supergirl and Mega Man defeats Proto Man and Dr. Wily, now Wily forces to give up once again.
Mega Man and other Superheroes returns back to their home of "The Justice of Superhumans".
Mega Man 2 Part 2: THE END