Often when I would be working on a storyline, I would have the story's basic structure in mind, but I wouldn't have the exact details, or individual comics, figured out yet. Then, as I would make the comics, I would wing my way through the basic ideas I had in mind, filling in the blanks. In this case, I think I alreay knew how I was going to end the storyline, but I didn't know how I was going to go about doing that, exactly.
In other words, I knew that Bob would end up being knocked into a portal that would take him on a series of trips through alternate dimensions, but I didn't know how I would be getting him into that portal. Bringing the Yellow Demon back, in the form of Nate, is something I would concoct later to make that plot point happen. In fact, according to an old IM conversation from around this time period, I had apparently considered having Bob fight the Author... and Bob might've won.
Anyway, usually when I was stuck like this, where I haven't quite decided how I'm going to get the characters where I want to them be later, I'd have a comic or two of inane stalling until I can figure it all out. Just think how much shorter the comic would be if I had actually planned everything out in advance.