Ms. Frizzle's class is learning about spiders. They take a trip to meet a spider expert, but she's missing. Then the bus turns into a moth and the class gets a very close look at some spiders and their webs.

As Ms. Frizzle leads the way, the class takes a journey through Arnold's digestive system, a pulsating excursion through Ralphie's bloodstream, and an exciting exploration through the Ralphie Robot to learn about bones, joints and muscles.

Ms. Frizzle takes the class on a camping trip, but Arnold is worried about monsters, and sets out to create a "Monster Scaring Perimeter" powered by a generator to keep the lights on--and in the process the class learns about sources of clean energy (and maybe monsters).

Ms. Frizzle takes the class on a trip to Hawaii, where the Magic School Bus provides them with individual submarines, and they learn about fish schools and the behavior of undersea animals--and try to avoid being eaten by a shark.