Bart pranks Principal Skinner by attaching superglue to his seat cushion and applying spray oil to the floor. Skinner sits in the seat, gets stuck, and then slips on the spray oil, falling down the stairs and requiring a trip to the hospital. Skinner demands a parent-teacher conference, which would be Bart's third one, and Marge would threaten to take away Christmas from Bart if he got three strikes. Bart runs away, with Milhouse joining him; hours later, they go to the port and sneak onto a ship.
Out at sea, Bart and Milhouse's voices can be heard on the ship, and the Sea Captain discovers them. With no way to get in contact with their parents, Bart and Milhouse are now part of the ship's crew. The first thing they do is make spinach, and Bart adds extra butter, ketchup, and sugar to it, causing the crew to get sick. Bart, Milhouse, and the Sea Captain all board a life boat and abandon the ship.
Back in Springfield, Marge and Luann are putting put flyers up, and Homer and Kirk get into a fight, forcing their wives to intervene. Bart, Milhouse, and the Sea Captain eventually land on an island, where they encounter monkeys. Two days later, the three make a treehouse, and eventually, Bart and Milhouse build a ship. Chief Wiggum calls off the search, and claims there is no more money in the city budget, but he and Lou drive off in a Batmobile.
Bart, Milhouse, and the Sea Captain sail off on the newly-built ship, which fills up with monkeys. Bart puts a large amount of salt and pepper in the bananas, which cause the monkeys to get sick. Once the monkeys finish throwing up, they chase Bart, Milhouse, and the Sea Captain off the ship, where they are stranded in the ocean. Arnie Pye sees them from his helicopter, picks them up, and returns them to Springfield. At Springfield Elementary, Milhouse receives the key to the school (which is made of chocolate) and Bart receives a back scratcher to scratch Skinner's back while he recovers from his injuries.