You know, looking at this Euclidean Found AU got me thinking some ideas. Wanna rune some by you to see if any are what you planned.
Instead of Bill being the villainous antagonist, it would probably be some ruler from the place trying to steal what Bill and Stanford are making.
The henchmaniacs, as we know in the show, have not yet met Bill, and it's instead a combination of Stanford's and Bill's research that causes them to come in contact.
The reasons that Bill was betrayed by his previous collaborators were the following: The shaman sensed the portal could unleash something reality couldn't handle and wanted to warn Bill about it, the Pharaoh felt challenged by Bill and his knowledge and tried to undermine him and his research, the mage just wanted to keep him as a pet to impress their love interest, and the anti-bill guy just became too paranoid about Bill and didn't belive the motive that he was trying to create a traversable portal to link the 2nd and 3rd dimensions together.