A gifted and smart young man tries to navigate life, puberty, and love while trying to survive his often dimwitted, dysfunctional family.
The family attends the counterculture Burning Man festival in the desert.
When Hal forgets to pay the family's health insurance, the company will not reinstate it until Monday, so he panics and locks the boys in their room to keep them from getting hurt.
When Hal catches Dewey smoking, he makes a deal with him that he will stop drinking coffee if Dewey quits smoking.
Reese and Malcolm try to perform the ultimate Halloween prank.
When Jessica goes through some family troubles, Lois agrees to let her stay at the house, making the boys crazy.
When Malcolm gets paired with a dimwitted beauty as his chemistry partner, he thinks it's a recipe for disaster, but when she reveals her feelings for him, sparks fly. They agree to keep their romantic experiment under wraps until Malcolm realizes that she's just embarrassed to be dating him. Meanwhile, Lois demands that Reese get a job, and she kicks him out of the house to prove that she means business.
Francis decides to surprise the family by coming home, and the power goes out in the house. Meanwhile, it's Lois who's in the dark when Hal decides to cancel their anniversary dinner in favor of a Reese-cooked meal at home. And Malcolm ends up in hot water after he sneaks three Dutch girls into the house.
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.
Lois thinks the new babysitter she found for Jamie is perfect... until she starts driving Lois crazy. Meanwhile, Reese starts getting picked on by the teacher when he and Malcolm are in the same class. However, Malcolm decides to defend him.
Malcolm receives a check for $10,000. After Hal and Lois find out, they decide to keep the money and spend it on something for themselves. However, when Dewey overhears this, he wants to get in on it, too. Now, they'll have to find a way to pay Malcolm back.
Lois, Hal, and Dewey go out of town for a piano competition, so they get Ida to watch over Malcolm and Reese while they're gone. Since Ida thinks Reese needs to become a man, she comes up with a competition for Malcolm and Reese, and if Reese wins, he can take Raduca as his bride. Now, when Lois and Hal return, they're surprised to find out that Reese has run away to Las Vegas to get married.
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.
Lois discovers she has mono after a visit to the doctor. She then ends up giving it to Malcolm after her maternal instincts begin. As a result, both Lois and Malcolm are forced to spend an entire day and night together in the same room. Hal, meanwhile, is invited to all of his neighbors' parties after they know Lois will not be attending any of them.
Hal learns that his father has passed away, but sheds no tears and passes it off as nothing since he never knew him. So, to make sure nothing like that happens again, he lets the boys do whatever they want by letting them miss school and even offering to buy Malcolm a new car, until Lois puts a stop to it. Noticing how depressed Hal has become, his friend Abe brings George Takei over for a visit in an attempt to cheer him up.
Francis receives a visit from Lois and Hal to celebrate his one-year anniversary of sobriety. However, when they attend one of his A.A. meetings, it's revealed that it was Lois who forced him to start drinking. Back home, Dewey finds Hal's spare key for his car and tries to get Malcolm and Reese to drive him to the arcade, but, of course, they refuse.
When four popular high school girls play an evil prank on Reese by pretending he has a secret admirer and then dropping a pig off at his front door, Lois comes to his rescue. She plots her revenge on the four unsuspecting girls and wreaks havoc on their adolescent lives. Meanwhile, Hal realizes Lois is at a dangerous emotional place so he decides to get some distance and stumbles upon the idea for making his own pitching machine out of stuff in the garage.
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.
Malcolm joins a local dance class to impress a girl, but when she loses her footing, he realizes that to win the competition he'll need a partner who can step it up. Dick, a rival student in the class who takes dancing a bit too seriously, challenges Malcolm to a dance-off. Meanwhile, Hal discovers an underground bachelor pad in the backyard.
When Stevie goes to the hospital, Malcolm tries making up every excuse he can think of to not go because he can't face the truth about his illness. Meanwhile, back home, Hal gets highly competitive about his new remote control boat, while Lois thinks she's going insane.
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.
For the senior prom, Reese gets paid to take Janine, a studious girl in class, but only after she gives him a makeover and sends him to finishing school, while Malcolm aligns with the unpopular kids to form an anti-prom they call "Morp." Unfortunately, while Malcolm and his friends protest the official dance, they don't know how to make their "Morp" exciting. Meanwhile, Dewey discovers there aren't any childhood pictures of him, so he concocts an elaborate scavenger hunt to punish Hal and Lois.
Malcolm struggles with his speech when he's elected valedictorian of his graduating class at school. However, Lois refuses to listen to any of his complaints and reveals that she wants him to become President of the United States. Meanwhile, Reese does everything he can to get a permanent job as a high school janitor, which includes creating the most disgusting mess ever. In the meantime, Hal has problems with Malcolm's Harvard tuition, while Francis finally gets a real 9-5 job that he actually enjoys. Also returning for the family celebrations is Grandma Ida, as they all say goodbye to Malcolm when he leaves for college.