One of the inherent problems with the Author pretending to be Mega Man is that he's the friggin' Author. There are only so many interesting storylines you can tell with an omnipotent main character. Battle getting too hard? Enemies too difficult? Snap your fingers, they cease to exist, end of problem. And the audience will never get a sense of danger from the comic when you know that nothing bad can happen.
Though, that being said, I think the audience eventually realized that while bad things do happen to the characters in the comic, they never actually die. Or if they do die, they're always brought back somehow. The downside to this is that much of the suspense of the storylines is diluted when you know nothing really bad will happen. I suppose that's one of the reasons to end the comic when I did. Eventually, the storylines would become boring and repetitive, since you know that no matter what happens, everyone will survive in the end. (You hear me, Marvel?)
Anyway, I knew the Author couldn't hang around in the comic much longer, but I needed him to replace Mega Man. The simplest solution, therefore, was to simply have Mega Man return. You know, I'm not exactly sure how Mega Man was able to kill this Yellow Demon in one blow, but if he could, why didn't he do the same thing when he and Proto Man face off against the next Yellow Demon? It's probably related to the RPG phenomenon where super powerful NPC's suddenly can't do any of their cool attacks once they join your party. In other words, Mega Man got nerfed.
Also, this is the only appearance of the 8-bit Yellow Demon. I hadn't started using Photoshop yet to resize some of the more cumbersome sprites, as evidenced by the ugly resizing of that sprite. I could go back and fix it, but I think it's a useful reminder of what happens when you don't resize in Paint by whole number increments.