To be totally honest about it, this entire part of the storyline really is rather ridiculous. I mean, Mega Man's running for some stupid reason, Bass is following them for some stupid reason, and I'm still not sure exactly why Proto Man's chasing after Mega Man, but while I'm pretty sure it's not entirely stupid, it's probably not very well thought out. And given that I was more or less making comics based on whims at this point, I hardly think character motivation was high on my list of things to worry about.
One interesting thing about this chase scene, by the way, is the visualization of their speed. Later on in the comic, if a character was moving fast enough, I'd just use a Photoshop blur to indicate their movement. Since I wasn't using Photoshop much yet, I resorted to using blur lines, which are actually used in Proto Man's sprite sheet. It's a little silly, but then again, this whole storyline is rather silly, so at least it fits.