Characters on Mega Man's side:
Nick Fury, Mega Man, Darci Roll, Supergirl, Black Panther (a new member), 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 (a new member), Cyborg, Captain America, Batman, Black Canary, Robin, Black Widow and Hawkeye
Characters on Luthor's side:
Dr Wily (hidden until tthe end of 1st part of Mega Man 4), Proto Man, Callisto, Lex Luthor, Mercy Graves, Pyro, Magneto, Lady Deathstrike, Dr. Doom, Electro, Green Goblin, Dr. Octopus, Bane, Dive Man, Drill Man, Toad Man, Bright Man, Pharaoh Man, Ring Man, Dust Man, Skull Man, Twin Robots (instead of being called for "Cockroach Twins") and seven of ED-209s (in Luthor's hands)
Mega Man 4: A New Evil Ambition (12th July 2065) (Over two years after Luthor's defeat in the last part of Mega Man 3)
Over two years after Lex Luthor's defeat, many thoughtthat Dr Wily was dead, after Luthor showed that he committed suicide. However, received a message from Luthor, who returns with Mercy Graves, Proto Man and new robots. Those new robot masters are Dive Man, Drill Man, Toad Man, Bright Man, Pharaoh Man, Ring Man, Dust Man and Skull Man, plus mini-bosses such as ED-209s to attack Metropolis. First of all Iron Man and War Machine defeats Dive Man. Then superheroes defeats other robots of Luthor's army;
Storm, Captain America, Cyborg, Mega Man and Black Canary defeats three first ED-209s
Human Torch and Supergirl defeats Drill Man
Iron Man and War Machine defeats 4th, and 5th ED-209s
Invisible Woman defeats Toad Man
Cyclops defeats Bright Man
Black Panther and Phoenix defeats Pharaoh Man
Supergirl, Mega Man and Cyborg defeats two last ED-209s
Mega Man defeats Ring Man
Batman and Robin defeats Dust Man
All those Superheroes defeats Skull Man. Then Iron Man and War Machine defeats Twin Robots (two other new robots in Luthor's army, and sent by him to attack those heroes). After defeating those robots Supergirl defeats Proto Man, then those Superheroes defeats Lex Luthor and Mercy Graves. Then forcing those two villains to surround. However, Lex Luthor reveals that Wily ordered him to scare people and attack "The Justice of Superhumans" by using those robots. Luthor gives up for now, those superheroes returns to home and are prepared for a new battle against Wily.
To be continued...