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

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.

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.

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.

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.

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.

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

Malcolm and the Krelboynes tutor Reese, and uncover the real reason behind his failing grades.

Hal is inadvertently responsible for a toxic chemical spill that forces a neighborhood evacuation; Malcolm deals with being grounded even in the emergency shelter; Francis suffers through a date with a geeky 12-year-old.

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.

In an effort to contribute to society and to make her boys useful at the same time, Lois "volunteers" Malcolm, Reese and Dewey for charity work at a local church. The boys are assigned to sort giant piles of donated clothing, game, appliances etc. Initially irritated at their new task, they realize the donated stuff is a lot nicer than their own possessions, and they begin swapping out their old stuff with the second-hand items. The boys soon make a enterprise out of their charity assistance, going as far as to sell things to the neighborhood kids - that is until Hal finds out. Meanwhile, Francis must come to grips with the fact his fabulous job in Alaska is not quite what he expected.

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.

The return of the smart and sassy Cynthia rattles Malcolm, who's astonished by her physical maturation. And so is drooling Reese.

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

High school's first day vexes Malcolm, who acquires an unfortunate nickname; and Hal, a parental "volunteer" running afoul of authority.

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.

Lois goes into labor while Hal and the boys are at a bridal exposition. Ida moves in after her apartment burns down and she refuses to stay with Susan.Dewey reveals the date his parents chose for the baby's planned delivery is his birthday in an announcement at the exposition to humiliate Hal.

While Lois is in labor, the house is hectic, and Hal, desperate to get home, has crashed the car on the way out of the expo.