Much like the original Star Fox on Super Nintendo, Star Fox 64's stages are split into three difficulty routes: Easy, Normal and Hard. However, unlike the original, SF64 only features two versions of Venom, one for the Easy Route and one for the Hard Route, the latter of which is where the Star Fox team has a final rematch with their rivals, Star Wolf.

It turns out the development team had planned on including another variation of Venom for the Normal route, where Fox McCloud would jump out of his Arwing and battle Andross on-foot with a bazooka. According to the staff, this was scrapped due to time constraints. The pilot mode option seen in Star Fox 64's battle mode is actually the repurposed remnants of this idea.