"The Mega Man of the past is broken and the Mega Man of the present must take his place."
The first enemy is Bubble Man, who tells Mega Man of the spikes. Mega Man challenges him to a jumping contest. Bubble Man finds out too late that he is too good of a jumper, hits the spikes, and dies. Mega Man gets his power to shoot lead bubbles.
The second Robot Master is Flash Man, but Mega Man confuses his name with that of the more... exposive flashers (No! Not that kind of "Flash" Man!). For some reason, his punches are ineffectual, even when Mega Man has been flashed. Mega Man shoots some lead bubbles at him, leading to a quick death. He acquires Flash Man's power.
Robot Master number 3 is Quick Man, who Mega Man accuses of being on crack, but he insists it's sugar, and thinks Mega Man will steal it. He is frozen by Flash Man's ability and dies simply from having to stand still. He gets Flash Man's super-speed.
Immediately after Flash Man's defeat, his brother Metal Man comes in to exact revenge. His first sawblade gets stuck in the panel edge (deja vu, it happened to Cut Man!), and his second deflects off the first one, bouncing around the panel edges and finally killing him. Mega Man gets his sawblades.
The next enemy is Wood Man (which, according to Mega Man, is another suggestive name). He is killed quickly by the sawblade weapon. Mega Man gets his Leaf Shield ability, but he doesn't know what the power even does yet.
The next Master is Air Man. He blows Mega Man away, but he clings onto one of Guts Man's blocks from the first game (which was just randomly sitting there). Instead of using a weapon, he gets into his time-travel suit and uses its jets to blast forward, but then Air Man jumps over and he hits the wall. When he comes back, he uses the Leaf Shield, but he didn't know what it was yet, and gets blown away again. Air Man starts inhaling (after Mega Man said "You suck."), giving Mega the chance to throw a leaf into his intake and explode. Mega Man gets the ability to shoot air blasts.
The next Robot Master is Crash Man (who Mega Man thinks is Clash Man). They have a chat about naming (Dr. Wily said "Bomb Man" was already taken.) and then he mentions that his bombs could be blown away by a small blast of wind. We don't see his death, but Mega gets Crash Bombs.
Mega Man meets Heat Man, and is about to use Crash Bombs, but the Author comes down saying that Crash Bombs didn't work for him in the game, so he can't use them. From what Heat Man said, Mega Man gets an idea to stuff Crash Bombs down his throat, which causes a gigantic explosion. Mega Man gets Heat Man's power (and survives the explosion, sent flying again).
Back at the lab, the past Mega Man is still under repair. Dr. Light then realizes that Mega Man's time-suit isn't completely time-proof, so he's slowly becoming defunct like the past one.
Mega Man flies past both Fortress Guardians (the dragon and Guts Man), avoiding a fight.
Back in the future, George complains about how temporal waves keep him blinking in and out of existance.
Back with Bob still trying to find his way back to the normal universe, he ends up in a universe where everyone talks Shakespearian language. He leaves.
Mega Man gets to Wily's fortress, where Dr. Wily is finishing cleaning his machine and starts charging his weapon. Mega Man gets ready for a dud shot, but Wily lets Mega Man take the first shot. He doesn't know that this Mega Man is from the future and can charge up his blaster. He destroys Wily's machine with one shot.
Wily then reawakens as an alien, but before he can take out Mega Man, Crash Man comes to stop him for giving him a stupid name (remember, his "death" wasn't shown?). Alien Wily is revealed to be a hologram and destroys Crash Man and is going to do the same with Mega Man, but X comes from offscreen and destroys Alien Wily. By now, the real Wily uncloaks himself while Mega Man is losing his memory. Wily orders Bass to kill them, but Mega Man tells Bass that the real Wily would say the security code before he gives orders (which he may or may not have made up due to memory problems). Bass then goes all-out on Wily.
Back at Dr. Light's lab, Wily claims to have amnesia and becomes Light's assistant again (which he is obviously faking). Mega Man, X, and Bass say their goodbyes and leave for the present time.