Characters on Mega Man's side:

Nick Fury, Mega Man, Darci Roll, Supergirl (later), Wolverine (later), Storm, Shadowcat, Rogue, Professor X, Ice Guy, Phoenix/Jean Grey, Beast, Cyclops, Angel, Nightcrawler, Mr. Fantastic, Invisible Woman (later), Harley Quinn (when she turns against Luthor), Deadpool (when he turns against Luthor), Cat Woman (later), The Thing, Human Torch, Spider Man (later), Iron Man, War Machine, Cyborg, Captain America, Batman, Black Canary, Robin, Black Widow and Hawkeye (later)

Brainwashed characters:

Invisible Woman, Supergirl, Wolverine, Spider Man, Harley Quinn, Cat Woman, Deadpool and Hawkeye

Characters on Luthor's side

Dr Wily (hidden), Proto Man, Callisto, Lex Luthor, Mercy Graves, Pyro, Magneto, Lady Deathstrike, Dr. Doom, Electro, Green Goblin, Dr. Octopus, Bane, Metal Man, Air Man, Heat Man, Flash Man, Bubble Man, Wood Man, Crash Man, Quick Man and Mecha Dragon

Mega Man 3: Luthor's Plot to Control Superheroes (1st july 2063) (About two months after Wily's defeat in the previous part of Mega Man 3)

Nearly two months after Wily's defeat, Lex Luthor and Mercy Graves doesn't either seem to be nice. Later, they'll brainwash six of Mega Man's, two of former Luthor's allies and one strange character, "Cat Woman". Those other brainwashed characters are Invisible Woman, Supergirl, Spider Man, Harley Quinn, Deadpool, Wolverine, Cat Woman and Hawkeye. However, Lex Luthor and Mercy Graves allows Mega Man 2 robot masters along with Proto Man to control them.

Mega Man and his allies (who aren't brainwashed) must confront against brainwashed heroes first (definitely without to kill them).

Batman and Captain America defeats Invisible Woman

Black Widow defeats Harley Quinn

Mega Man and The Thing defeats Deadpool

Robin defeats Cat Woman

Captain America defeats Wolverine

Batman defeats Hawkeye

The Thing defeats Spider-Man

Black Canary and Mega Man defeats Supergirl. After defeating those brainwashed Superhumans, those brainwashed went to hospital. However, those superheroes who weren't brainwashed, will continue to new battles. But this time they continuing this to battle Mega Man 2 robot masters;

War Machine defeats Bubble Man

Mega Man and Cyborg defeats Flash Man

Black Canary and Mr Fantastic defeats Wood Man

Ice Guy defeats Heat Man

Iron Man and Angel defeats Air Man, then defeating Crash Man

Mega Man defeats Metal Man

Captain America defeats Quick Man.

After defeating Mega Man 2 robot masters, those Superheroes defeats Mecha Dragon, which they previously defeated from Mega Man 2 Part 2.

Storm defeats Callisto

Ice Guy defeats Pyro

Wolverine defeats Lady Deathstrike

Human Torch and Captain America defeats Dr. Doom

Mega Man defeats Electro

War Machine defeats Green Goblin

Spider-Man and Cyborg defeats Dr. Octopus

Batman and Robin defeats Bane

Mega Man and Supergirl defeats Magneto

Then those heroes also defeats Proto Man, Mercy Graves and Lex Luthor.

Now, those heroes goes home to the "Justice of Superhumans".

Mega Man 3: Luthor's Plot to Control Superheroes: THE END