"Bob shows up in the past to save his brother while Mega Man kicks butt."
Shadow Man is about to finish off Mega Man, but Bob comes in, asks where Dr. Wily's fortress is, and leaves. Mega Man suddenly wakes up and tries to switch weapons, but the weapon module is broken and he lands on Top Spin. Shadow Man is afraid of the Top Spin for some reason, and runs away from the fight.
At Wily's lab, George is still hanging, and Wily is about to start construction on his Doc Robots, but Bob is now storming the fortress. Wily says he'll give George back if Bob kills Mega Man. He agrees.
Mega Man is now about to fight Spark Man, but he is hiding while Spark Man laments about having no hands. Then Mega Man tries to throw a shuriken, but it doesn't affect Spark Man. After saying Light could give him hands, Spark Man tries to lift the shuriken with his long stubs. He succeeds, but ends up short-circuiting.
In the present, Roll and Proto Man don't like their current coffee break; they aren't doing anything! So we cut to Mega Man and Bass, about to jump off a cliff ("something stupid" again). They do it (the spiky rocks broke their fall), and they find Mike, still alive.
In the past, Mega Man is going to fight Snake Man, and he's cloaked with Shadow Man's power again. But Snake Man's Search Snakes find him, knocking him off the wall. They prove to be ineffectual in actual fighting, however, so Mega kills them all with the EMP. Snake Man was grounded, though, so he survives and beats up Mega. Mega Man then uses BOLT 3 (Spark Man's power, also a Final Fantasy reference) to kill Snake Man. He gets the "Search Snakes".
Bob is now going through the Robot Masters, catching up to Mega Man, but to his horror he finds Top Man and Alternate Bob dancing.
Mega is now reading the strategy guide, saying that he should beat Gemini Man, then Needle Man. He tosses the guide, killing a Met.
Now Mega has arrived at Needle Man's area, full of smoke from his drugs. His first hit on Mega gets him into a drug-induced coma. In the coma, he meets Ran for the first time and leaves the coma, after throwing Ran (with his huge Cossack Buster out) at Needle Man. He wakes up and finds that he basically nuked Needle Man, and heads to the next boss.
Mega meets Break Man again, but he leaves because Mega Man was too rude and unfollowing in the previous encounters.
Mega runs into the next Robot Master/Masters, Gemini Man. They start arguing about which one is the clone, and start using their dancing Gemini Laser attack. One accidentially blabs that their weakness is Search Snakes, so Mega Man summons up two giant-sized Search Snakes to kill both of them. He aquires the Gemini Laser.
Mega returns to the lab to give Dr. Light the Power Crystals retrieved while killing the Masters.
At Wily's lab, Dr. Wily begins construction on Doc Robot while Proto Man and George talk. Wily also decides to equip Doc with the powers of all Robot Masters he made thus far.
Wily returns to Light's lab to take over Gamma...