Parallel stories pit Malcolm against a bullying, obnoxious new kid and Francis vies with his intimidating, military-school commandant, who's presenting sex-education lectures. Meanwhile, Hal takes heat after cutting down a tree.

While Hal secretly takes the boys to the stock car races, Lois desperately searches for her missing paycheck. Francis at military school is keeping a boa constrictor as a pet.

A spiffy cheerleader attracts slovenly Reese, who cleans up his act—best as he can—to woo her. He even joins her rah-rah squad. Dewey tries to convince Lois and Hal to buy him a new toy. Francis has a heart-to-heart conversation with headmaster Spangler.

Malcolm and his Krelboyne classmates enlist the help of Hal for a school project, which involves a robot, and an enormous swarm of bees. Lois visits Francis at his school after he becomes injured and soon clashes with Spangler.

When the family goes to a water park for a day, Dewey is left home with an elderly, stern babysitter. Francis is hustled at pocket billiards by his military-school commandant.

Shenanigans abound at the fancy spot where the family's dining with the Kenarbans, and at Francis' school, where rowdy teenage girls are partying.

Malcolm gets a role in the high school play and is so captivated by high school gossip that he forgets his lines. Lois discovers the joys of massage. Hal and Dewey build a society of model buildings in the living room. Francis tries to show his individualism at school when the commandant cracks down on personal belongings.

Dewey starts carrying a purse to school. Francis's friend Richie joins him at military school. Malcolm becomes a slave to an old woman in the neighborhood.

Lois and Hal try to end Dewey's dependence on his stuffed animal Domingo by convincing him that it is too dirty. Strangely attracted, Malcolm finds himself in emotional confusion about the new weird Krelboyne girl Cynthia. At the academy Commandant Spangler re-institutes old Hickory into the school's disciplinary system and Francis tries to convince his father Hal to lie for him to avoid punishment.

New neighbors, who turn out to be even more awful than Malcolm's family, move in next door; the Marlin Academy cadets prepare for a visit from Oliver North.

A hospital stay unsettles Malcolm, who's stuck in a kids ward with what may be appendicitis. Meanwhile, at military school, Francis leads a hunger strike.

Lois forbids the boys to ride a motorbike they found, but Reese disobeys and breaks a leg.

The family takes a vacation with the Kenarbans, sharing a houseboat. And while Steve's parents are caught in a fight, Reese and Steve socialize with some cheerleader from a nearby spirit camp, Malcolm is stuck with Hal fishing. At the military academy, Eric turns eighteen and leaves for Alaska, inspiring Francis to do something about his situation too.

Being fed up with military school, Francis gets himself legally emancipated so he can go north to Alaska with his friend Eric and become a logger. This does not sit well at all with the family.

Dewey rules, thanks to his new dog that intimidates Malcolm and Reese; Hal and Lois hit the town with big plans---and flu symptoms.