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.

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.

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.

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.

Francis visits the week after Halloween and helps his brothers in a trick that involves a giant slingshot with icky ammo. Hal tries to catch a mysterious hot-rodder.

Hal and Lois heads off to a convention while the boys stays home for the babysitter. Malcolm, Reese and Dewey assumed it's just another old woman, their parents hired to watch them. They decide to do a series of pranks on their babysitter, which includes the covered up sewer tank with a blanket and a book for the old woman sit on. To their surprise, their babysitter is a hot, teen-aged girl named Patty. She is sweet to them, but also bitter because she was rejected by Francis, a long time ago, because she was obese. Now the boys compete against each other to see who will prove their eldest brother wrong in his rejection and sleep with her without sex. Meanwhile at the convention, Lois tries in vain to stop the fight between Hal and Jack, who stole his idea.

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.

Hal feels like his job is a piece of c* after going to Dewey's class for parent job day. So he decides to take a "kidney failure" weeks off. While Francis is forced to work at the lucky aid over spring break.