Malcolm finds his life as the middle brother in an eccentric family made even more difficult by his being placed in a class for gifted students at school where he reluctantly befriends another boy with a high IQ and stands up to a bully.

Lois and Hal leave the boys alone for the weekend with Francis. the boys assume that if all goes well, Francis may not have to go back to military school.

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.

Malcolm's cushy babysitting job provides relief from the trailer the family's using while their house is being fumigated, until Malcolm learns that the trust placed in him in his new position is strictly limited. Meanwhile, the military school's master key leads Francis to a corpse, for which he provides a proper send-off.

Malcolm sleeps over at Stevie's house and, appalled at his over-protected lifestyle, persuades him to sneak out to a strange, late-night escapade. Francis deals with hazing at military school. Reese tries to prove he's man enough to watch a scary movie.

Francis goes AWOL from military school to link up with his girlfriend, a ditsy doozy who's made him gaga.

The whole family attends a Krelboyne family picnic, and Malcolm dreads his performance in the event's Academic Circus will make him look like a freak. Disasters abound as stage acts bomb, families feud, and Malcolm's dad serves meat to vegetarians.

Lois's firing prompts household economizing. Meanwhile, Francis delights in his honor-guard duty—at a teenage beauty pageant.

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 relative's funeral conflicts with Malcolm's plans for his very first date, so he tries to figure out a way to skip the bereavement ceremony.

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.

Roller-skating lessons from Hal bug Malcolm, who rebels against dad's discipline while mom agonizes in bed from a backache she blames on Reese. Francis avoids his squad's survival weekend.

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.

The boys stay home from school when their mother thinks it's Sunday instead of Monday. Malcolm thinks of a plan to get Francis out of trouble once again. Hal gets sucked in by a Porsche dealership.

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.