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.

Kitty returns and asks Lois for help getting Kitty's estranged husband back; Francis comes home and puts Dewey through the torturous "Brotherhood Initiation."

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.

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

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.

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.

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 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.

When Hal and Lois realize how little time they spend together, Hal turns the garage into a private tiki lounge where he and Lois can retreat. Things go smoothly until they feud over philosophical beliefs. Meanwhile, Mr. Herkabe cons Malcolm into joining the Booster Club, where he learns a lesson about taking one for the team.

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.

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.

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.

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.

When Dewey's pet rabbit does good in a state contest, the family must travel to Las Vegas for the nationals. But Reese unknowingly sells the rabbit to a restaurant. Now it is up to Dewey (with a little help from a "choking" Reese) to try and save the rabbit. Meanwhile, Malcolm tells Hal and Lois that they embarras him, and that is why he didn't tell them he won state science honors. As a form of repayment, Malcolm gets great seats for him and Lois to see Lois' favorite singer. Lois then gets lucky and is invited backstage where all she really wants to do is figure out why Malcolm doesn't want her around. Hal, on the other hand, is looking all across Las Vegas for a slot machine that he has had dreams of winning the jackpot on. Francis is also in trouble when he gets behind on duties at the ranch, and for the first time sees that Otto isn't just a pushover for everything.

Jamie's babysitter coerces Malcolm into doing a "small" task for her; Dewey finds a friend, only to lose him to Reese; Francis persuades Otto to confront an old adversary that once courted Gretchen.

When Lois tracks down her father's "other family," she meets Victor's "other wife" Sylvia, and learns something shocking about her dad.

Lois thinks Jamie is out to get her when Jamie knocks over a shelf and nearly crushes her.