The family’s misadventures continue as Malcolm faces new challenges at school and home. Reese explores his culinary talents, Dewey’s imagination runs wild, and Francis’s escapades at military school add to the family’s chaos.
Hal, Loi, Malcolm and Reese are trapped in a horrendous traffic jam. Francis enters himself in a bet that recalls the egg-eating wager in "Cool Hand Luke." Malcolm becomes smitten over a girl he meets. Dewey has his own little adventure--all over the world--before his family returns home.
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.
A family weekend vacation to a casino turns into an ordeal in the desert for Hal, Reese and Malcolm, who wander onto an artillery range. Francis sneaks home, but has no one to play with.
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.
The night shift at Lucky Aide is held hostage by two robbers, since Craig does not want to give up the combination for the store's safe. Francis tries to help a heartbroken friend at the academy, while Hal and the boys fight nature at home.
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.
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.
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.
Lois' estranged parents, Ida and Victor, pay the family a visit. Right away, trouble starts brewing. Victor bonds with Reese, Ida gets Malcolm into a fight, and Dewey is haunted by childhood memories of his inattentive grandparents.
Lois gets a traffic ticket and immediately blames Francis and makes him get the money to her. To do this, Francis stages a stunt for the other cadets' amusement. Malcolm finds evidence that Lois was wrong about the traffic ticket.
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.
Francis has an extra ticket for a wrestling event and it is the prize pitting Malcolm vs. Reese in a one-upmanship war; caring for Craig's cat is troublesome for Dewey.
Malcolm, Dewey, Stevie, and Reese hide out at a traveling carnival after hours and run afoul of a determined security guard and several members of the freak show.
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.
Lois is two weeks late with her period, causing her and Hal to panic and start a big fight, while trying to keep it from the boys. And while Dewey is scared that his parents may split up, Hal and Lois remember the troubles of getting their previous four sons.
