Alright, the basic plot was about an evil man named Werner Warner
who -- in revenge against Ms Frizzle for spurning his advances when they were both younger
(Ms. Frizzle had yet to come out of the closet)
-- sabotages the magic school bus so, when her class gets on board for another one of their wacky field trips, it transforms into a starship and blasts off into deep space, getting lost in uncharted territory in the process.
As this story was heavily inspired by the sci-fi films I'd seen at the time -- the Star Wars Trilogy and the Lost in Space film, to be specific -- a lot of the plot and motifs mirror those movies; while the class gets stranded on a planet inhabited by Klingons
(actually Ferengi, but I didn't know their real name at the time)
who ride rancors -- and while the unspoken love between Arnold Perlstein and Phoebe Terese begins blossoming into full romance
(Phoebe and Arnold in earlier, orangier, times)
-- Werner Warner uses his powers in the dark side to conquer Earth and establish an ersatz Empire complete with ersatz stormtroopers to serve him and enforce his will.
(Werner Warner following his rise to power (minus the red lightning bolt emblem I envisioned on his chest))
Eventually, after escaping the shockwave of an exploding planet
(I would have used a screencap from the ending of Lost in Space, but I couldn't find one)
Ms. Frizzle and her class returns to Earth, but the magic school bus is shot down by an ion cannon blast.
Once they fall to Earth, they are all captured by Warner's ersatz stormtroopers and the bus is blown to hell with a laser bazooka.
Later on, Frizzle and the kids escape imprisonment, and Arnold -- with a blue lightsaber he got from somewhere (can't remember where exactly) -- has an encounter with Warner, who weilds a red lightwhip. The two duel, and after Arnold pulls Warner's lightwhip out of his hands and sends both energy weapons plummeting down a power shaft, an explosion occurs which seemingly kills Warner and brings his ersatz Empire to an end.
(it's a climax similar to this, just much, much stupider)
Long story short, everyone lives happily ever after. Ms. Frizzle even collects the obliterated magic school bus' key, which she plans on using to create a new magic school bus.
(Did I unconsciously lift a plot element from this movie? God, but I feel soiled again ...)