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
Characters on Wily's side:
Dr Wily, Proto Man, Callisto, Deadpool, Harley Quinn, Lex Luthor (secretly), Mercy Graves (secretly), Pyro, Magneto, Lady Deathstrike, Dr. Doom, Electro, Green Goblin, Dr. Octopus, Bane, Magnet Man, Hard Man, Top Man, Snake Man, Shadow Man, Spark Man, Gemini Man, Needle Man, Metal Man, Air Man, Heat Man, Flash Man, Bubble Man, Wood Man, Crash Man and Quick Man
Mega Man 3: Rise and Fall of Dr. Wily (6th may 2063) (Over three years after Wily's punishment in the end of Mega Man 2 part 2)
Two years after Wily's punishment, Wily was freed from his cell by Lex Luthor and claimed he was a changed man. Luthor, Mercy Graves and Wily began to create new robot masters; Magnet Man, Hard Man, Top Man, Snake Man, Shadow Man, Spark Man, Gemini Man and Needle Man. A year later, those robots are completely created. However, those robots goes out of control and start attacking (at least scare them away) humans. Mega Man along with other superheroes returns to defeat those robots and villains.
First Supergirl confronts and defeats Proto Man in 1st fight. Then Supergirl, Mega Man and Batman defeats Magnet Man.
After defeating Magnet Man, Supergirl confronts and defeats Proto Man again in 2nd fight. Then Supergirl, Iron Man, Human Torch, Invisible Woman and Spider-Man defeats Hard Man.
After defeating Hard Man, Nightcrawler and Cyclops defeats Snake Man, while Supergirl defeats Top Man. Then Supergirl confronts and defeats Proto Man again in the 3rd, and last fight. Now they are confronting those last four robot masters;
Batman and Robin defeats Shadow Man
Black Widow and Hawkeye defeats Spark Man
Jean Grey/Phoenix and Rogue defeats Gemini Man
Captain America defeats Needle Man.
However, even those robot masters defeated, there are still eight more. They're robot masters who those Superheroes previously confronted; Metal Man, Air Man, Heat Man, Flash Man, Bubble Man, Wood Man, Crash Man and Quick Man. Now the battle continues;
War Machine defeats Bubble Man
Cyborg and Invisible Woman defeats Flash Man
Mega Man defeats Metal Man
Spider-Man defeats Quick Man
Black Canary and Hawkeye defeats Wood Man
Ice Guy defeats Heat Man
Angel and Iron Man defeats Air Man, then defeating Crash Man.
After defeating those robot masters (originally from Mega Man 2), Supervillains returns to confront those Superheroes.
Storm confronts and in last defeats Callisto
Mega Man and Captain America defeats Deadpool
Black Widow defeats Harley Quinn
Ice Guy defeats Pyro
Wolverine defeats Lady Deathstrike
Mr. Fantastic and Invisible Woman defeats Dr. Doom
Spider-Man defeats Electro
War Machine defeats Green Goblin and Dr. Octopus
Batman and Robin defeats Bane
Supergirl and Black Canary defeats Magneto. Then those heroes also defeats Proto Man, and in last also defeats Dr. Wily (with his own ship). Wily fell from the ship, unharmed, he runs away. A day later Luthor shows a video in the "News" there Wily commits suicide, he also says "I'll allow Lex Luthor to take over my robots". Whatever, someone claimed that Wily faked his own death, and also claimed to hear that Wily ordered Luthor to create a copy or hologram of himself.
To be continued...