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, Guts Man, Cut Man, Elec Man, Ice Man, Fire Man, Bomb Man, Titanium Man, Pyro, Magneto, Lady Deathstrike, Dr. Doom, Electro, Green Goblin, Dr. Octopus and Bane

Mega Man Part 2 (June 2057) (Nine months after Wily's defeat)

Mega Man was created by Nick Fury and born in the year 2056, to defend the humanity from half-evil Dr. Wily. However, nine months later he returns with Proto Man, same supervillains, and seven robot masters. Six of them are same robot masters, who superheroes previously confronted, but Wily did also bring a new robot master called "Titanium Man".

However, a war returns with Dr. Wily, Proto Man, Pyro, Magneto, Lady Deathstrike, Dr. Doom, Electro, Green Goblin, Dr. Octopus, Bane and those seven robot masters. Mega Man along with other superheroes returns to defeat those robots and villains.

Batman defeats Elec Man

Nightcrawler defeats Fire Man

The Thing, Supergirl and Iron Man together defeats Titanium Man

War Machine defeats Bomb Man

Invisible Woman and Human Torch defeats Ice Man

Mega Man and Spider-Man defeats Cut Man

Supergirl and Guts Man confronts each other, however, Harley Quinn and Deadpool unexpectedly defeats that robot.

After defeating those robot masters, Pyro, Magneto, Lady Deathstrike, Dr. Doom, Electro, Green Goblin, Dr. Octopus and Bane comes to confront those heroes.

Mr. Fantastic and Invisible Woman defeats Dr. Doom

Mega Man defeats Electro

Batman and Robin defeats Bane

Ice Guy defeats Pyro

Rogue (Jean Grey) defeats Lady Deathstrike

Spider-Man defeats Green Goblin

Cyborg and Wolverine defeats Dr. Octopus

Storm and Supergirl defeats Magneto.

Then Iron Man and Supergirl together defeats Proto Man and Dr Wily, which forces him to give up.

Mega Man and other Superheroes returns back to their home of "The Justice of Superhumans".

Mega Man Part 2: END