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.

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.

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.

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.

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.

Malcolm's humiliation as a Krelboyne drives him crazy, so he fakes his way into seeing the school's shrink, with whom the con continues.

Reese, promising champion of his school's wrestling team, gets beaten by a girl, completely demoralizing him. So he gives up his school-bully carrier, which destabilizes the natural order of things at school. Francis tries to get out of academy at his birthday in an attempt to avoid academy-birthday-traditions.

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.

A cooking class energizes Reese; a planned party irks Malcolm, whose brutal honesty hurts the hostess, Krelboyne Cynthia.

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.

Francis has to stay a couple of days in a small county jail and enjoys it more then he expected. Malcolm finds himself with a girlfriend, which add to his usual social anxiety. Dewey makes friend with a new kid in the area, helping the kid's mother to compose Dewey's dream birthday party for his new friend.

Trouble finds Reese at his new fast-food job; a new Krelboyne tutors Malcolm; Hal and Lois sabotage Dewey's plan to get a dog.

Back in the general school population, the Krelboyne whiz kids wind up in cliques with jocks, skateboarders and brooding "Goths."

An academic competition faces the Krelboynes in an event Malcolm derides. Especially when he learns his teacher has a cheating plan. Also: a commitment to a formal dance ruffles Reese, who's now trying to ditch his date.