Characters on Mega Man's side

Nick Fury, Mega Man, Proto Man, Eddie, Rush, Darci Roll, Supergirl, Black Panther, Wolverine, Storm, Shadowcat, Rogue, Professor X, Ice Guy, Phoenix/Jean Grey, Beast, Cyclops, Angel, Nightcrawler, Mr. Fantastic, Invisible Woman, Harley Quinn, Deadpool, Cat Woman, The Thing, Human Torch, Spider-Man, Iron Man, War Machine, The Penguin, Cyborg, Captain America, Batman, Black Canary, Robin, Black Widow and Hawkeye

Characters on Wily's side

Dr Wily, Bass, Treble, Callisto, Pyro, Magneto, Lady Deathstrike, Dr. Doom, Electro, Green Goblin, Dr. Octopus, Bane, Lex Luthor, Mercy Graves, ED-209s, Blizzard Man, Centaur Man, Flame Man, Knight Man, Plant Man, Tomahawk Man, Wind Man, Yamato Man, Samuraibots (in NES-version "Ben Ks"), Drillbots (in NES-version "Molier"), Rounder 2-bots and Ride Armored Met Z

Mega Man 6: Luthor's Revenge (15th October 2068) (Over a year after Decepticon's defeat, prior to Mega Man 6)

Over a year after Megatronus and Wily's defeat, Lex Luthor, Mercy Graves, Magneto and Bass were invited in a robotic tournament, their robot masters are Blizzard Man, Centaur Man, Flame Man, Knight Man, Plant Man, Tomahawk Man, Wind Man and Yamato Man. Their robots won in Metropolis, few hours later they went berserk, adding mini-bosses like ED-209s, Samuraibots and Drillbots. Justice of Superhumans (including Mega Man) were sent again, this time even Proto Man is one of the heroes. Then the heroes meets some of those robots.

Ice Guy defeats Flame Man.

Batman defeats Plant Man.

Human Torch defeats Blizzard Man. Then Iron Man and War Machine defeats 1st ED-209.

After defeating 1st ED-209, Iron Man, Angel and War Machine defeats Wind Man.

Deadpool and Harley Quinn tries to provoke Centaur Man, while they do that, Invisible Woman quickly defeats Centaur Man.

After defeating Centaur Man, Iron Man, War Machine and Black Canary defeats first five Drillbots. Then Supergirl confronts and defeats Knight Man.

After defeating Knight Man, Mega Man, Deadpool and Nightcrawler defeats first three Samuraibots, while Proto Man defeats the second ED-209. Then Mega Man defeats Yamato Man.

After defeating Yamato Man, Iron Man confronts and defeats Tomahawk Man.

However, Mega Man confronts Bass for the first time. After the confrontation, Mega Man wins his first round. Bass says "Round 1 goes to you, Mega Man"

After defeating Bass in round 1, Iron Man and War Machine defeats Rounder 2-bots, on a building. Then Iron Man, Invisible Woman, War Machine, Mega Man, Proto Man and Captain America defeats other five Drillbots and two Samuraibots.

Mega Man confronts Bass once again, in last he even defeats him again.

After defeating Bass in second time, heroes together confronts and defeats Ride Armored Met Z. Then Hawkeye and Black Widow goes after Luthor. Black Widow defeats Mercy Graves, Hawkeye defeats Lex Luthor and forces him to give up. A moment later, Wily shows up himself and reveals that he is behind LexCorp's attacks. Now, Hawkeye and Black Widow leaves Luthor, and Mercy Graves for now. Hawkeye and Black Widow reveals about this thing, Wily's mastermind of LexCorp, for the other members of Justice of Superhumans.

To be continued...