The Magic School Bus Inside the Human Body is the third book in the book series.
After Ms. Frizzle teaches her class about the human body, she shrinks them and the bus, except Arnold, who swallows them. This gives Cole and Degen a chance for two parallel stories, inside and outside of Arnold. With the bus inside, Cole explains digestion from the stomach into the small intestine. Then the bus enters a blood vessel where readers can see the plasma and red and white blood cells and they flow into the heart. From there the class, now out of the bus and garbed in operating room smocks and masks, flow with the red blood cells, now with fresh oxygen, to the brain. They climb down the bones of the spine, follow nerves to see muscles work, and then finally catch up with the bus to emerge into the nasal cavity. Meanwhile on part of the facing page, Arnold has coped with being lost and alone and has made it back to the school. With an enormous sneeze, he sends the bus out to join him in the parking lot. The class can now chart the body from actual experience.
From the TV episode "For Lunch", If you pause at the right time, you can see Arnold inside the shrunked bus.