So, the original plan was to get Bob to the Megaman Universe and hope that the forces there could subdue him. If not, George was supposed to leave Bob behind and seal the portal behind, at the very least trapping Bob forever in another dimension. And while George initially lied to both Mega Man and Bob about their purpose in the Megaman Universe, Bob has clearly figured out the truth and is planning to turn the tables on them by trapping George in the Megaman Universe instead.
Now, initially, I thought this would be a bad thing. I mean, without George around, who would be able to stop Bob from running loose? I was thinking that George was the only thing stopping Bob from taking over completely, and at the beginning of the comic, this may very well have been the case. But looking back from the end of the comic, I see a serious flaw with this idea. If George's powers don't affect Bob, George is the one person that is completely useless against Bob. So George's presence in his home dimension doesn't really change anything.
Although, I suppose having someone around who isn't affected by Bob's powers would be pretty handy, at least in a support position. Every D&D group needs a healer, right?
And while I'm on the subject of things I didn't think through, I never did explain how Bob figured out what the plan was. Perhaps his post-portal confusion simply wore off and he put two and two together.