Characters on Mega Man's side
Nick Fury, Mega Man, Sigma (in the ending, instead of being an antagonist, he will be a great protagonist from now through Mega Man X-series), 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
Neutral
Callisto, Pyro, Magneto, Lady Deathstrike, Dr. Doom, Electro, Green Goblin, Dr. Octopus, Bane, Lex Luthor and Mercy Graves
Characters on Wily's side
Dr Wily, Bass, Treble, Proto Man, Vile, Zero, Nail Man, Tank Man, Jet Man, Glue Man, Trinitro Man, Rainbow Man, Yo-Yo Man, Comet Woman, Block Man (in the NES-version of Mega Man Unlimited called for "Yoku Man"), Hammer Man, Container-throwing Cardriving Mets, Mega Tanks, G-soldiers, Scorpionbots, Tank Joes and Laser Drone
Mega Man 10: Mega Man's Final Battle?! (earliest 25th August 2074) (over three months after Wily's defeat in the previous event of Mega Man 10)
Over three months after Wily's defeat, Wily returns with his new robots. Once again, they're attacking Metropolis, Proto Man tries to find out what it is. But then Proto Man is kidnapped by one of Wily's robots.
After Proto Man is kidnapped, Mega Man along with the heroes returns back to confront those hostile robots, but soon a new friend of Mega Man will arrive. Then Angel, Iron Man and War Machine confronts and defeats Hammer Man.
Captain America and Supergirl defeats Nail Man.
Iron Man and War Machine defeats Tank Man. Then Iron Man, Mega Man, Spider-Man and War Machine together defeats two Mega Tanks, four Tank Joes and three G-soldiers.
Black Canary and The Thing defeats three Container-throwing Cardriving Mets. Then Iron Man defeats Jet Man.
Human Torch and Ice Guy defeats Glue Man.
Storm, Invisible Woman and Iron Man together defeats four Scorpionbots. Then Iron Man and War Machine defeats Trinitro Man.
Iron Man and War Machine defeats Laser Drone. Then Mega Man, Cyclops and Supergirl defeats Rainbow Man.
Wolverine defeats Yo-Yo Man. Then Iron Man, Angel and War Machine defeats Comet Woman.
In last Invisible Woman defeats Block Man. Then all of those heroes together defeats Proto Man (because of he was reprogrammed and thought of his father's (Dr Wily) survival) and Bass.
After defeating Bass and Proto Man, Zero appears. First Mega Man tries to stop Zero, but Zero is too skilled and dangerous for him. Mega Man's left arm ends up being chopped off by Zero. Just before Zero can take him to prison (or finish him off, if he is a threat to Decepticons and Dr Wily), Mega Man's new friend arrived just in time. The robot's name is "Sigma". Sigma threatens to attack Zero more if he doesn't surrender, which forces Zero to do it along with Proto Man and Bass. Wily gives up for now.
Few days later, when the heroes and Mega Man already returned. But Sigma also appears, he presents himself to Mega Man. Sigma tells Mega Man, that he in this time needs to be upgraded to "Mega Man X". Unlike prior times, it will be another fight, but those times he will be more advanced than he was before.
First he will be trained to win over copies of Mega Man 10 robot masters, then few years later begin with his missions to confront Wily and his more aadvanced robot masters.
Mega Man 10; Official: THE END