As the family drives home from the water-park, they get stuck in a traffic jam. While each family members tries to deal with heat, stress and boredom in their own way, Dewey is roaming the country on his own.
Francis is a week late for Halloween, but that can not stop him from traditional festive vandalism, since he has the perfect plan to cause mischief in the neighborhood. Meanwhile Hal has to fight a different neighborhood nuisance, vigilante style.
When Lois gives the boys $10 each to buy her a present, they decide to get something for themselves, which causes her to have grief. When Hal also forgets her birthday, Lois decides that is enough, so she escapes until the family finally decides that they need her. Meanwhile, Francis brings home a beautiful African woman.
Commandant Spangler announces his mother's visit and Francis uses the opportunity to organize a dance, for which he invites some local girls, which ends up to be a very different experience then the cadets expected. Meanwhile the Kenarbans invite the whole family to a nice dinner that turns into an evening of conflicts, as the families get to know each other better.
The family is on a weekend-vacation in an native American casino. Francis uses this opportunity to go on vacation himself, by sneaking into his former home, but he is not the only one with that idea. While Hal, Reese and Malcolm get lost in the desert, Lois and Dewey enjoy a day of relaxation.
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 ...
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.
In an attempt to avoid the worst moments of medieval week at his Krelboyne class, Malcolm spins a delicate web of deception for the school therapist. Francis takes over the laundry at the academy and Hal discovers that his youngest, Dewey, is a natural at skittles.
Malcolm gets the chance to perform at a high-school play in the lead role, leaving his friends alone with their secret project. But hanging out with high-school kids and their constant exchange of useless information has quite an impact on Malcolm's mental abilities. Lois finds herself with twenty five unexpected free minutes left on her schedule, which she uses for a massage, relaxing for the first time in her life. Hal and Dewey build a giant city out of Lego, while Francis tries to fight Commandant Spangler's tyranny with flower power.
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 oder of things at school. Francis tries to get out of academy at his birthday in an attempt to avoid academy-birthday-traditions.
Malcolm accidentally hits a ball into grouchy old Mrs. Griffen's yard and, when going to retrieve it, he has a run-in with the old lady, accidentally making her fall and break her arm. As punishment, Malcolm must go over to Mrs. Griffen's house every day after school to help her out; Dewey begins carrying a purse to school rather than a back pack; Francis must deal with his screw-up friend Richie at military school.
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.
A new family moves into the next house and the family tries to make friends with them. As it turns out, all but the two men despise each other, which leaves them living their new-found friendship in secrecy. Francis finds Commandant Spangler emotionally devastated, questioning his own accomplishments, comparing himself to a prominent visitor to the academy.
Hal feels like his job is a piece of crap 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. To make matters worse, Grandpa Victor gives Reese a live grenade as a present, and worse comes to worse, the boob pulls the pin! Luckily the family survived the explosion, but their brand new, expensive refrigerator wasn't as lucky.
Francis organizes a hunger strike to get back the academy's TV, taken away by Commandant Spangler. Meanwhile Malcolm has to go to the hospital, leaving him in the children's ward and the family without their genius middle son.
In an attempt to change the usual punishment pattern for Reese, Hal signs them both up for cooking classes, which turns out to be Reese's area of genius. Meanwhile Francis gets Eric into trouble because he did not yet finish his part of their co-op history assignment. Malcolm has the best intentions when he tries to explain to Cynthia that her planned party might end up with less then expected attendance.
Francis is home to repair the roof, while Reese has even more troubles with his grades then usual, although he is convinced that his Teacher Mr. Woodward is out to get him. While Dewey makes a new friend, Lois makes Malcolm tutor Reese and Malcolm soon finds out that Reese was right about Mr. Woodward all along.
In this special episode, we see what would happen if Lois took the kids bowling and what would happen if Hal took them bowling. Lois keeps the kids under tight watch, making Malcolm's night miserable, since he's the worst bowler in the group; Hal is on the verge of a perfect game, Reese ticks off the wrong guy and runs for his life, and Malcolm finds a girl who is attracted to him.
In this episode Craig still lives in Lois and Hal's house, because his one had been burnt down. That costs a lot of things on the whole family. Meanwhile, Malcolm and his brothers find a mini-bike in the garbage. At first they argue with each other, but after their mother banned the use of the bike, they join forces against her. At the same time Hal goes to Allabama to visit his son Francis for the Fathers-and-Sons meeting, where he expects some great achievements from his son. But what will happen after all that ?
When the family gets a new couch, Hal loses the old one on the way to the dump, causing a train accident with dire consequences for the whole neighborhood. While Hal tries to make it up to society, Dewey makes people believe he is an orphan. Reese starts a black market, while Malcolm is grounded and confined to the bunk in the emergency camp. Meanwhile Eric takes Francis on a somewhat different double-date.
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.