Hal and Lois are penning their will, and think back to all the trouble their sons put them through. It is there that Lois' problems with Francis are finally revealed and how her inability to admit when she is wrong lead to a lot of the problems the family has been dealing with.

An embattled psychiatrist probes the boys' naughty behavior patterns in a session framed by flashbacks to past episodes.

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.

Shenanigans abound at the fancy spot where the family's dining with the Kenarbans, and at Francis' school, where rowdy teenage girls are partying.

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.

Clever Hal invigorates Dewey's soccer team; sly Reese blackmails a philandering neighbor; obsessed Malcolm battles a computer program.

Malcolm is convinced to play Softball by Lois and ends up doing very badly at it due to Lois's hold on him. Meanwhile, Francis tries to pick fights with Lois, Reese tries to break Francis's record of collecting toilet seats from a local junkyard, and Hal accidentally applies to become a member of the CIA.

Reese meets a cute vegetarian named Carrie when he goes back to work at the meat plant. At first, he goes along with her political talk, but she catches him with a pork chop. So, to get Carrie back, he sets free all the cows at the meat plant. Malcolm, meanwhile, tries to fool Lois in order to attend a rock concert.

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

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.

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.

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.

With the arrival of their fifth child, Lois and Hal search for a "creative" daycare solution.

Hal sets up Abe Kenarben on a blind date with Jaime's babysitter Polly but then realizes Lois has also set her up on a blind date - with Craig. Malcolm, Dewey (with his "lucky" shirt) and Reese also meet Reggie Jackson and Francis is embarrassed by Piama in front of his co-workers.

A broke Francis gets talked into getting a real job by Dewey, but one of Francis' rocker friends decides to offer him the position of tour manager of his band instead. Back home, Hal takes over the college recruiters, which Malcolm refuses to meet with, and treats each one as a suitor. However, Hal's plans are ruined when Malcolm chooses to go Harvard.

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.

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.

The family takes a vacation with the Kenarbans, sharing a houseboat. And while Steve's parents are caught in a fight, Reese and Steve socialize with some cheerleader from a nearby spirit camp, Malcolm is stuck with Hal fishing. At the military academy, Eric turns eighteen and leaves for Alaska, inspiring Francis to do something about his situation too.

Lois, in an attempt to get a break from the family, joins a book club that turns out to be a night off for frustrated housewives, but it all goes a little bit haywire. Meanwhile Francis tries to get to Alaska, learning something important about himself and about truck drivers. Hal, who tries to keep the boys out of troubles for the evening, is caught in an inner conflict about how to treat them.

The arrival of Francis's new bride on Hal's birthday sparks a fray that drives the younger siblings out---and into a posh hotel.

After Lois is out of town, Malcolm and Hal got into a fight leading Malcolm to get expelled from his house. Malcolm lives with his girlfriend in her attic, as Hal put signs for "Missing Malcolm."

Malcolm tries to emancipate Dabney from his overbearing mother while Hal invites his ne'er-do-well old buddy to the house. At the ranch, Francis is forced to share a room with Otto.

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.

When Hal and Lois go out of town for a "last chance" getaway before the baby comes, Reese has a big bash that gets out of hand. College-age thugs show up, cancel the party and set up a drug-making operation in the garage. All Reese and Malcolm can do is knuckle under. The good news is, Dewey's not around. The bad news is, his baby sitter is Lois's annoying co-worker Craig. Meanwhile, Hal and his very pregnant wife are off at a romantic retreat---feuding.

Leonard, a cynical, genius chess player with no friends or job, makes Malcolm think he could grow into a similar adulthood. Determined to prevent this undesirable fate, Malcolm tries to help Leonard change his life by lining him up for a job interview with the obnoxious Craig. Meanwhile, Francis finds employ as a nude model and begins to delight in the exposure.