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.

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.