The Wilkerson boys plan to sneak off to a New Age festival in the hope of seeing some naked women, but when their parents find out, the trip becomes a family affair. Malcolm falls for an older woman, while Lois goes topless after discovering the joys of hemp.

Hal forgets to pay the family's health insurance and when the company won't reinstate them until Monday, he panics and locks the boys in their room so they won't get hurt. But the boys try to escape, Jamie gets in harm's way and Hal is the one who needs a doctor. Meanwhile, Lois and her coworkers discuss unionizing at the Lucky Aide and she hits her 10-year anniversary at the store.

When Hal catches Dewey smoking, he makes a pact with him that he'll stop drinking coffee if Dewey kicks the habit, but after a few unsuccessful attempts to beat their addictions, they both start sneaking around. Meanwhile, Reese picks a fight with Stevie and their confrontation gets heated

Malcolm and Reese go on a tour of the neighborhood for Halloween, but get scared when their own house is the first stop on the tour.

The neighbor's daughter, Jessica, stays with Malcolm and the family for a week. She soon shows Malcolm how to manipulate Lois to get what he wants. Also, Reese gets into a fued with his foreign penpal and Hal tries to avoid a confrontation with a... bee!

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, but he catches Jamie off-guard and ends up knocking the lights out in the house. Meanwhile, it's Lois who's in the dark when Hal decides to cancel their anniversary dinner and forces Reese to cook them a romantic feast at home, and Malcolm who ends up in hot water when he sneaks three Swedish 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 finds a new babysitter for Jamie who is wonderful until she opens her mouth and starts to drive Lois crazy. Meanwhile, Malcolm and Reese are in the same class, but Reese is the one being picked on by the teacher - until Malcolm stands up for him.

Malcolm gets a check for his college fund but never sees it as Hal and Lois intercept. A debate soon erupts over what they should do with it (new water pipes or a boat) until someone else wants in. Meanwhile, Reese gets into (and causes) trouble when he starts hanging out at the nursing home.

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 ,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 heads back to work at the meat plant and meets Carrie, a cute vegetarian. He pretends to go along with her politics, and he almost pulls it off until he's caught red-handed with a pork chop. To get Carrie back, Reese goes to the plant and sets all of the cows free. Meanwhile, Malcolm tries to pull the wool over Lois' eyes and sneak off to 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.

Recently elected valedictorian of his graduating class, Malcolm struggles with his speech, but Lois refuses to hear his complaints and reveals her plans for him to become President of the United States. Meanwhile, Reese will do anything to get a permanent job as the high school janitor, even concocting the most disgusting mess of all time, which explodes all over the family. At home, Hal struggles with Malcolm's Harvard tuition and Francis lands a "real" job working 9 to 5 in a cubicle and enjoys every minute of it. Grandma Ida returns for the family festivities, and they all bid farewell to Malcolm when he leaves for college.