Bart brings Santa's Little Helper to school for Show & Tell. However, the dog gets into the air duct and causes chaos in the school, just as Superintendent Chalmers comes for an inspection. Skinner is fired and Bart feels guilty.
Ned Flanders replaces Skinner as Principal, but has trouble keeping order. Meanwhile Seymour and Bart become friends, and spend a lot of time together. Skinner decides to re-enlist in the army, but Bart misses him and comes up with a scheme to get Skinner back into the school: showing Chlamers how bad the school is under Flanders' authority.
Chalmers is unfazed by the chaos, until he hears Ned sharing a prayer over the tannoy. Chalmers fires Ned and rehires Skinner as Principal - but now he and Bart must become enemies again.