See? What, four comics of his recolored regular sprite, and he changes right back. What a waste of time.
Anyway, Mega Man presents a good point here. Yes, they have a time machine, but what good is a time machine if they don't know where to go? Are they supposed to check every moment in all of time, trying to find out where the Bass went?
I suppose if they wanted to be smart about it, they would start jumping back in time at regular intervals until they reached a point in time where things are the way they're supposed to be, and then narrow down on the disruption. You know, something like a binary search algorithm. But that seems like an awful lot of work, especially for this comic.
An even better approach would be to jump back to the moment Bass entered the portal, and then either scan the portal and figure out where it goes or just go into the portal themselves. Though, if they accidentally disrupt the portal and somehow prevent Bass from going back in time at all, they'd certainly prevent the paradox, but create another one in the process... Freaking time travel...