A gifted and smart young man tries to navigate life, puberty, and love while trying to survive his often dimwitted, dysfunctional family.
When Reese realizes the Army is too much for him to handle, he deserts and dresses as an Afghani woman. But Lois is on a march to find him, and travels to Kabul to hunt him down. Meanwhile, Malcolm volunteers at a veterans hospital as a way to make up for his guilt of making Reese leave.
The Buseys disappear after Dewey leaves the special-needs class; Hal becomes the leader of a group of brainless bodybuilders.
When Hal and the garbageman get into a trash-dumping war (which benefits Dewey more than anyone else), Hal enlists Reese's help. Meanwhile, Lois gets her job back at Lucky Aide (off probation), and fights against Malcolm in order to take down an offensive billboard of a smiling black janitor (whose nametag reads "Slappy") holding a mop and a 6-pack of malt liquor. Soon it's an all-out war between mom and son - until Lois encounters a fellow employee who is more racist than the billboard.
Malcolm and Reese plot revenge after they realize their teenage neighbor has tricked each of them into believing the other is gay. Meanwhile, Hal, tired of competing with a neighbor who always outdoes his Christmas decorations, decides to create his own "holiday" to decorate his house for - Pearl Harbor Day.
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 and Lois, strapped for cash, decide that Christmas gifts will have to be homemade this year. When everyone makes much better gifts than Hal, he spins a bigger and bigger lie about the present he has in store for them. In desperation, Hal pick-pockets Malcolm's secret credit card, and buys the family a ski vacation.
Hal is sleepless because of their upcoming 20th wedding anniversary. So he ask Reese for some ideas for presents. Then Reese gets the idea to brainwash his dad while he's nervous. Dewey's friends are set up in an upcoming student body election when a bully nominated two of his geeky friends. Malcolm takes up playing the electric guitar, though Lois discourages his musical ability. He writes a heart warming song. When he plays & sings his creation, Dewey figures out that his song is sung to the tune of the "Meow Mix" jingle!
Lois thinks Jamie is out to get her when Jamie knocks over a shelf and nearly crushes her.
When Malcolm spots a roughed up 1967 Cuda in his neighborhood, he instantly falls in love with it and purchases the car. But he gets so caught up in the difficult task of restoring it that he blows off Stevie as well as Reese who needs him for an illegal betting scheme of his. Hal on the other hand, is having success when he stumbles upon his hidden talent -- hairstyling. Lois doesn't have time to worry about Malcolm or Hal, as she is caught up in scandal between Craig and their Lucky Aide boss Fred. Craig says he is taking time off to tutor Fred's wife in golf but Lois finds out he is actually having an affair with her.
When Lois catches the boys vandalizing a trashy billboard for a strip club, Malcolm alters the vandalism into a women's rights protest, which sparks a colossal media circus. In no time, feminists, conservative religious groups and national new reporters descend on the scene. After Hal grants a TV interview, a woman from his past turns up at the faux protest; and Reese, inspired by the giant billboard stripper who comes to life in his dreams, gives an impassioned speech about the objectification of women.
When Lois buys a brand-new king-sized bed, Hal thinks that her motive is to put more distance between them and refuses to sleep in it. Moved to tears by an opera he sees on television, Dewey is inspired to write his own operatic masterpiece, "The Marriage Bed," which is based on his parents' fight and turned into a school production. Meanwhile, Malcolm and Reese build their own street luge board; and Jamie falls head over heels for the baby girl across the street.
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.
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.
During Grandma's unwelcome visit with the family, she loses her leg while saving Dewey from a moving truck. Consumed with guilt, Dewey is determined to find his Grandmother's leg and give it the proper burial. Francis, on the other hand, begrudgingly becomes the caretaker for his stubborn, cranky grandmother. Meanwhile, Malcolm and Reese are given a new idea for a prank that forces them to stay awake days at a time to avoid the embarrassment of having their faces glued to the floor.
After Hal forbids Dewey from inviting his peculiar classmate Chad over for a sleepover, Dewey quickly finds out that his father had good reason to warm him. Meanwhile, Malcolm and Reese find out that they are not as popular as they once thought, then plot "revenge" on their classmates.
When Francis and Piama choose to celebrate Francis' 21st birthday at the house, Hal is reminded of a promise he made to his son as a young child, involving a motorcycle trip that Lois quickly forbids. Hal and Francis have no choice but to sneak off for their wild adventure, leaving their women behind. Meanwhile Malcolm, Dewey and Reese are held captive in their own home by a bully.
Malcolm discovers a man, Norm, living in the Lucky Aide. He agrees to keep Norm's secret as long as he provides Malcolm with tidbits on his new crush, a fellow Lucky Aide employee. Meanwhile, when Reese takes a job as an exterminator, he quickly learns that to drum up business he must infest the neighbors' lawns, and chooses caterpillars as his weapon. But instead of spreading the caterpillars, he has a change of heart and begins to nurture them, ultimately leading to his own menagerie of butterflies.
Lois goes over to visit Ida, but gets unpleasantly surprised by the St. Grotus Day festival. Malcolm fails a music appreciation course, and reluctantly goes to Dewey for help. Reese and Hal secretly watch scary movies while Lois is not around, but it ends up revealing some unexpected secrets about both Reese and Hal.
Reese befriends a pack of troublesome stray dogs; Dewey feels conflicted when he starts seeing another mother-figure; Hal unwittingly becomes a motivational speaker.
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.
When Hal decides to attend his first annual Neighborhood Association meeting with Malcolm, he is strongly encouraged to take on the role of President. Being his dad's right-hand man, Malcolm sees a perfect opportunity to add some excitement to the community, while Hal's agenda is a little bit different. Meanwhile, Francis takes on a new job as a camp activities coordinator and turns to Dewey for his input on some creative new games. While Dewey revels in his afternoon of fun, his fed-up classmates take their teacher, principal and janitor hostage.
Unbeknownst to Lois, the boys enter her in the Mrs. Tri-County Pageant as a joke. When they overhear the other contestants remarking that Lois doesn't have a chance of winning, they plot to help their mother take the crown. Meanwhile, Malcolm is blackmailed into delivering love notes to a contestant for Herkabe, and Reese discovers that, according to the Mrs. Tri-County Pageant manual's scientific formula, he is beautiful.