So, if we're going through this whole backstory thing again with Mega Man instead of the Author, then this comic would be the remake of this comic. Part of the joke, then, is that Mega Man doesn't seem to have a problem being broken up into billions of molecules and transported as energy. Clearly the Author is a giant wuss for screaming. Further, Mega Man isn't scared of a few minor robot minions.
Further, this comic clearly shows that regardless of how stupid Mega Man may act most of the time, he's still a bad-ass with his blaster. And after as many video games as Mega Man has been in, you'd probably be a bad-ass too. Personally, I like to think of Mega Man as the epitome of a kick-ass fighting robot, with a 100% accuracy rate and maximum efficiency out of every shot. You know, since he's got a computer for a brain and I can't see a computer wasting any energy when destroying things. You know, basically the exact opposite of how I actually play the games.
Oh, and in case you're wondering, I decided to start with Cut Man because I always start with Cut Man when I play the first Megaman game. I think I read it in a strategy guide somewhere.