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.

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.

When Lois finds renewed energy with orthotic inserts for her shoes, Hal fears she will not look to him for support anymore and plots to destroy the inserts. A former female army buddy of Reese's comes to their house for a visit. But she gets defensive when Reese thinks they are way more than just friends and comes intact to the idea of trying to sleep with her.

Hal's friend Trey tells him to come to his dental office when he looses a tooth during a poker game, but their friendship becomes in jeopardy when Hal's faced with a $2,000 bill and causes a fight between them. Reese, meanwhile, teaches Lois how to ride a bike, while Malcolm and Dewey find sleeping as their new favorite pastime.

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.

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

After Lois and Hal are reminded of the tight budget they must uphold, Hal discovers one of his boys has been dialing a 900 number. His attempt to explain the error to the hotline's billing department turns awry when he forgets to hang up the phone, incurring a whopping $800 charge. Meanwhile, Reese takes a job at a research clinic that pays him to pop experimental pills, and a reluctant Malcolm takes on a mortifying job at the Lucky Aide as a costumed Uncle Sam on stilts.

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

Acting dumb like Reese eases Malcolm's stress and lands him a date with the new light of his life, an attractive girl who's really a dim bulb.

Hal and the boys offer to watch baby Jamie so an exhausted Lois can finally get some sleep. Hal leaves the boys in charge while he goes to the Lucky Aid to pick up more diapers. While the boys are watching Jamie, three beautiful teenage girls arrive and woo Malcolm, Reese and Stevie away for the night, leaving Dewey alone with the baby. Meanwhile at the Lucky Aid, Hal doesn't have enough money for the diapers and Craig forces him to work. Back at home, Dewey concocts an elaborate bedtime story for Jamie involving each member of his family.

Neighbors have the annual "The Wilkersons are gone" block party until they come home early. Reese and Dewey set up a plan to get money by letting Reese-tortured kids get revenge. Hal and Lois enter a kielbasa-eating contest and Malcolm unknowingly assists a robbery, but a surprising twist comes in the end.

Malcolm gets his tongue pierced and needs to hide it for a month. While Lois' mother, Ida, comes and annouces that she will marry a rich Chinese Man that she met on a cruise. Malcolm gets complications when his tongue ring gets infected, rendering him unable to say "S's" and he discovers that Ida has been drugging her fiancé with opiates and mood enhancers. When Lois and Hal confront Ida, she drugs them with free food. But luckily, the fiancé misses a drug treatment, and realizes that Ida is a terrible woman and he leaves her at the altar. Malcolm is punished for his tongue piercing. Meanwhile at the ranch, Otto decides to hire a murder mystery acting troup, but it all turns out badly.

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.

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.

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.

Lois gets jury duty and Hal tries to figure out what case she's working on. Meanwhile, Malcolm and Reese saw Stevie's mom naked and brag about it, they also take Dewey to the sewers and get lost.

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.

Hal is named executor of his neighbor's living will and must decide whether to keep him on life support or pull the plug. In attempting to make the decision, Hal discovers he is incapable of making decisions on his own because he always defers to Lois. Meanwhile, Craig asks Malcolm, Reese and Dewey to teach him how to fight dirty since a bully from his childhood is coming to town.

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.

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.

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.