"Bob ends up in the Rockman Universe, where things are normal."
This storyline starts with Mega Man destroying Junk Man in a Robot Master palace. Then Guts Man comes in and starts to kill Mega Man, but then the battle freezes, and it seems that it was a computer simulation Roll was running (she didn't like to see him get beat up). The computer alerts of a possible intruder in sub-section 3-C.
Bob is the intruder, and Mega tells his true name as Rock Man, and proceeds to call Bob "Blues" with a different color scheme. Bob then talks with his conscience and finds out he wandered into the "proper" universe, the Rockman Universe.
They rush off to Dr. Right (they can't tell Right or Light due to his speech impairment). Bob makes fun of his impairment, and Roll pushes him into the kitchen before Dr. Right has an aneurysm.
Roll starts feeling irritable while Rock Man has a sudden like of ice cream, and Bob believes he's corrupting the universe.
Meanwhile, the Author and the Shadowy Author end up at another time, where the sky is blue with gray ground. This isn't the Cataclysm, but the Shadowy Author states that he needed to make a stop. Another Author pops from the top of the screen, supposedly the one in the present, and he explains the The Attack of Mega Man storyline briefly ("Well, Mega Man turned evil and tried to kill everyone.") He leaves to move on the storyline.
The Shadowy Author shows up to the universe Bob is in, but finds everyone dead except Bob, who killed them because they were corrupted. It turns out that the Author was corrupting them, not Bob, and the Shadowy Author resets everything Excel Saga-style. Bob then runs away. Right afterward, Dr. Wily contacts everyone saying that he kidnapped Blues (who is this universe's Proto Man), but there is still the deal that Bob (everyone thought he was Blues!) was just there, and it generates a lot of confusion for both parties. Rock goes to save Blues, and gets kidnapped himself. Roll freaks out at the message; she wasn't programmed to deal with this type of situation.
At Wily's lab, Blues has escaped, and Bob has killed off Wily's team of sniper robots. Wily brings Rock to a test machine, and duplicates Rock Man into himself and an evil clone, and they start fighting. Someone makes off with Forte (Bass).
A Christmas special (in the normal universe) interrupts the comic.
Bob then properly introduces himself to Rock and kills Forte and the Rock clone. The laser, however, doesn't work on Bob; he's not a robot.
A New Year's special in the normal universe interrups the comic.
Bob is then faced with a gigantic army of Rock clones, but he nukes the whole fortress.
Rock has arrived there, and realizes that Bob isn't a robot, so he's fully qualified to kill people. He then realizes that he doesn't have a dreaded archnemesis, so he has nothing to do. Bob solves the problem by sending Rock on a trip to the tropic island of Acapulco.