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, Elec Man, Ice Man, Fire Man, Bomb Man, Metal Man, Air Man, Heat Man, Flash Man, Bubble Man, Wood Man, Crash Man, Guts Man, Cut Man, Quick Man, Water Man, Volt Man, Dyna Man, Titanium Man, Mecha Dragon, Pyro, Magneto, Lady Deathstrike, Dr. Doom, Electro, Green Goblin, Dr. Octopus and Bane
Mega Man 2 Part 2 (15th April 2060) (Over seven months after Wily's defeat in the previous part of Mega Man 2)
Over seven months after Wily's defeat in the previous part of Mega Man 2, he returns again with Proto Man, supervillains, those robot masters (all those who appeared, for the first time, in those varying four previous times in the past) and a new gigantic flying robot, a "Mecha Dragon". Mega Man along with other superheroes returns to defeat those robots and villains. First, Iron Man and War Machine defeats Bubble Man. Then other Superheroes defeats other robots such as;
Batman defeats Elec Man
Human Torch defeats Ice Man
Cyborg and Invisible Woman defeats Flash Man.
Ice Guy defeats Fire Man, then defeating Heat Man
Angel defeats Bomb Man, then along with Iron Man defeating Air Man and Crash Man
Mega Man defeats Metal Man
Captain America and Spider-Man defeats Wood Man
Supergirl and Black Canary defeats Titanium Man. Then those heroes also faces three robot masters;
Supergirl and Mega Man defeats Guts Man
Invisible Woman defeats Quick Man
Wolverine and Spider-Man defeats Cut Man. Then they're defeating three more robot masters;
War Machine defeats Water Man
Batman, Robin and Spider-Man defeats Volt Man
Beast and Mega Man defeats Dyna Man. After defeating those robots, those superheroes defeats the Mecha Dragon and then those Supervillains;
Ice Guy defeats Pyro
Wolverine defeats Lady Deathstrike
Mr. Fantastic and Invisible Woman defeats Dr. Doom
Batman defeats Electro
War Machine defeats Green Goblin
Spider-Man defeats Dr. Octopus
Robin defeats Bane
Supergirl, Mega Man and Iron Man defeats Magneto. After defeating them, those heroes defeats Proto Man and Dr Wily. When Wily is defeated, he won't be allowed to control robots in at least 3 years. Those robots which Wily controlled would be handed over to Nick Fury. Two years later Fury allows Luthor to take over all those robots if he isn't freeing Wily, or even allow Wily further a year later, if he's a changed man.
Mega Man 2 Part 2: THE END