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, Water Man, Volt Man, Dyna Man, Pyro, Magneto, Lady Deathstrike, Dr. Doom, Electro, Green Goblin, Dr. Octopus and Bane
Mega Man Part 3 (Sep 2058) (A year and three months after Wily's last defeat from the previous part of Mega Man 1)
A year and three months after Wily's last defeat, he returns with Proto Man, same supervillains, and three new robot masters. Those new robot masters are Water Man, Volt Man and Dyna Man.
However, a war returns with Dr. Wily, Proto Man, Pyro, Magneto, Lady Deathstrike, Dr. Doom, Electro, Green Goblin, Dr. Octopus, Bane and those three robot masters. Mega Man along with other superheroes returns to defeat those robots and villains. First Iron Man and War Machine defeats Water Man. Then other superheroes defeats other robot masters;
Batman, Robin and Spider-Man defeats Volt Man
Mega Man and Supergirl defeats Dyna 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.
Iron Man defeats Dr. Doom
War Machine defeats Green Goblin
Spider-Man defeats Dr. Octopus
Mega Man and Hawkeye defeats Electro
Batman and Robin defeats Bane
Ice Guy and Storm defeats Pyro
Wolverine defeats Lady Deathstrike
Supergirl and The Thing defeats Magneto.
Then those superheroes defeats Proto Man and Dr Wily, which forces Wily to give up again.
Mega Man Part 3: END