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.
22 minS1:E1
Pilot
Malcolm finds his life as the middle brother in an eccentric family made even more difficult by his being placed in a class for gifted students at school where he reluctantly befriends another boy with a high IQ and stands up to a bully.
Lois and Hal leave the boys alone for the weekend with Francis. the boys assume that if all goes well, Francis may not have to go back to military school.
Parallel stories pit Malcolm against a bullying, obnoxious new kid and Francis vies with his intimidating, military-school commandant, who's presenting sex-education lectures. Meanwhile, Hal takes heat after cutting down a tree.
Malcolm's cushy babysitting job provides relief from the trailer the family's using while their house is being fumigated, until Malcolm learns that the trust placed in him in his new position is strictly limited. Meanwhile, the military school's master key leads Francis to a corpse, for which he provides a proper send-off.
Malcolm sleeps over at Stevie's house and, appalled at his over-protected lifestyle, persuades him to sneak out to a strange, late-night escapade. Francis deals with hazing at military school. Reese tries to prove he's man enough to watch a scary movie.
The whole family attends a Krelboyne family picnic, and Malcolm dreads his performance in the event's Academic Circus will make him look like a freak. Disasters abound as stage acts bomb, families feud, and Malcolm's dad serves meat to vegetarians.
While Hal secretly takes the boys to the stock car races, Lois desperately searches for her missing paycheck. Francis at military school is keeping a boa constrictor as a pet.
A spiffy cheerleader attracts slovenly Reese, who cleans up his act—best as he can—to woo her. He even joins her rah-rah squad. Dewey tries to convince Lois and Hal to buy him a new toy. Francis has a heart-to-heart conversation with headmaster Spangler.
Roller-skating lessons from Hal bug Malcolm, who rebels against dad's discipline while mom agonizes in bed from a backache she blames on Reese. Francis avoids his squad's survival weekend.
Malcolm and his Krelboyne classmates enlist the help of Hal for a school project, which involves a robot, and an enormous swarm of bees. Lois visits Francis at his school after he becomes injured and soon clashes with Spangler.
The boys stay home from school when their mother thinks it's Sunday instead of Monday. Malcolm thinks of a plan to get Francis out of trouble once again. Hal gets sucked in by a Porsche dealership.
When the family goes to a water park for a day, Dewey is left home with an elderly, stern babysitter. Francis is hustled at pocket billiards by his military-school commandant.
Hal, Loi, Malcolm and Reese are trapped in a horrendous traffic jam. Francis enters himself in a bet that recalls the egg-eating wager in "Cool Hand Luke." Malcolm becomes smitten over a girl he meets. Dewey has his own little adventure--all over the world--before his family returns home.
Francis visits the week after Halloween and helps his brothers in a trick that involves a giant slingshot with icky ammo. Hal tries to catch a mysterious hot-rodder.
A family weekend vacation to a casino turns into an ordeal in the desert for Hal, Reese and Malcolm, who wander onto an artillery range. Francis sneaks home, but has no one to play with.
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 will prove their eldest brother wrong in his rejection and sleep with her without sex. Meanwhile at the convention, Lois tries in vain to stop the fight between Hal and Jack, who stole his idea.
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.
Malcolm gets a role in the high school play and is so captivated by high school gossip that he forgets his lines. Lois discovers the joys of massage. Hal and Dewey build a society of model buildings in the living room. Francis tries to show his individualism at school when the commandant cracks down on personal belongings.
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 order of things at school. Francis tries to get out of academy at his birthday in an attempt to avoid academy-birthday-traditions.
Dewey starts carrying a purse to school. Francis's friend Richie joins him at military school. Malcolm becomes a slave to an old woman in the neighborhood.
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.
New neighbors, who turn out to be even more awful than Malcolm's family, move in next door; the Marlin Academy cadets prepare for a visit from Oliver North.
Hal feels like his job is a piece of c* 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.
Lois gets a traffic ticket and immediately blames Francis and makes him get the money to her. To do this, Francis stages a stunt for the other cadets' amusement. Malcolm finds evidence that Lois was wrong about the traffic ticket.
A hospital stay unsettles Malcolm, who's stuck in a kids ward with what may be appendicitis. Meanwhile, at military school, Francis leads a hunger strike.
Francis has an extra ticket for a wrestling event and it is the prize pitting Malcolm vs. Reese in a one-upmanship war; caring for Craig's cat is troublesome for Dewey.
Malcolm, Dewey, Stevie, and Reese hide out at a traveling carnival after hours and run afoul of a determined security guard and several members of the freak show.
Hal is inadvertently responsible for a toxic chemical spill that forces a neighborhood evacuation; Malcolm deals with being grounded even in the emergency shelter; Francis suffers through a date with a geeky 12-year-old.
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.
The family takes a vacation with the Kenarbans, sharing a houseboat. And while Steve's parents are caught in a fight, Reese and Steve socialize with some cheerleader from a nearby spirit camp, Malcolm is stuck with Hal fishing. At the military academy, Eric turns eighteen and leaves for Alaska, inspiring Francis to do something about his situation too.
Being fed up with military school, Francis gets himself legally emancipated so he can go north to Alaska with his friend Eric and become a logger. This does not sit well at all with the family.
Lois, in an attempt to get a break from the family, joins a book club that turns out to be a night off for frustrated housewives, but it all goes a little bit haywire. Meanwhile Francis tries to get to Alaska, learning something important about himself and about truck drivers. Hal, who tries to keep the boys out of troubles for the evening, is caught in an inner conflict about how to treat them.
Francis has to stay a couple of days in a small county jail and enjoys it more then he expected. Malcolm finds himself with a girlfriend, which add to his usual social anxiety. Dewey makes friend with a new kid in the area, helping the kid's mother to compose Dewey's dream birthday party for his new friend.
In an effort to contribute to society and to make her boys useful at the same time, Lois "volunteers" Malcolm, Reese and Dewey for charity work at a local church. The boys are assigned to sort giant piles of donated clothing, game, appliances etc. Initially irritated at their new task, they realize the donated stuff is a lot nicer than their own possessions, and they begin swapping out their old stuff with the second-hand items. The boys soon make a enterprise out of their charity assistance, going as far as to sell things to the neighborhood kids - that is until Hal finds out. Meanwhile, Francis must come to grips with the fact his fabulous job in Alaska is not quite what he expected.
When Hal's doctor discovers something suspicious during his routine check-up, Lois and Hal become frantic, nervous wrecks as they wait for the test results. As a result of her anticipation, Lois becomes even stricter with the boys, leaving them to misinterpret the new house rules. Meanwhile, in Alaska, Francis comes to blows with his boss.
When Malcolm and his brothers destroy their Christmas tree ornaments, Lois punishes them by canceling Christmas and moves all the presents into the garage. The only way she will reinstate the holiday is if the boys behave impeccably up to Christmas morning. Her plan works better than expected, and Lois is touched that her family responded so well to her challenge. Meanwhile, the boys decide that Lois could use this tactic for future holidays and retaliate by breaking into the garage and opening up all the presents. Elsewhere, Francis is forced to visit his Grandma Ida for Christmas.
Juicy guest casting and ingenious plotting enliven an hourlong episode that airs in the plum post-Super Bowl slot. One storyline unfolds at Hal's company picnic, where Lois clashes with a blabby wife and her beleaguered spouse; and Hal runs afoul of his new boss and the big cheese. In Alaska, Francis's scheme to win a bet involves rigging a hockey game that pits loggers vs. a fearsome women's squad led by a blowhard coach.
After Hal is mistaken by his new boss, as that guy's boss, Hal plays along. Malcolm is in a three-legged scavenger hunt with the girl he likes, but becomes upset after he confesses he likes her, and she says she likes another boy. Reese is also the the scavenger hunt, and at first doesn't like the big dumb bully he is with, but they grow to like each other when they bond over beating up the other contestants and stealing their items. Lois continues to balance keeping Dewey intact and dealing with the crazy woman, but now must talk to the husband as well. Francis continues to sabotage his own team, this time on the ice.
Lois gets jury duty and Hal tries to figure out what case she's working on. Meanwhile, Malcolm and Reese saw Stevie's mom naked and brag about it, they also take Dewey to the sewers and get lost.
Malcolm, whose frenetic home life is a kind of zoo, begins the fourth season by accompanying his family to the real thing. A visit to the zoo offers close encounters with creatures great and small. But Hal wishes he could have passed on an encounter with Lois's former beau, who lectures on rain-forest animals. Elsewhere, Reese butts heads with a goat; and Malcolm and Dewey take a tumble into a tiger den. Another storyline checks in on ne'er-do-well Francis, now the unlikely foreman of a dude ranch owned by a cheery German businessman.
Christopher Lloyd adds to his gallery of eccentric characters, playing Hal's quirky, cranky and very wealthy father, Walter, in this rollicking episode. The occasion is a birthday celebration for the old man, but the snooty female in-laws seem more interested in offending Lois. Their shabby behavior initially goes unnoticed by Hal, who's desperately trying to bond with his self-centered dad; and by Dewey and Reese, who seek some of Grampa's dough by currying favor with him. But when Lois is reduced to tears after being excluded from a group photo, the family rallies to her side with an all-out counterattack that turns the party into pandemonium.
Malcolm starts to date Nikki. Meanwhile, Hal and Lois must take abstinence pills in an attempt to be better parents. At the ranch, Otto is furious with the other ranchers who keep destroying the fence that Francis is building to keep the cattle inside.
After joining the basketball team at school, Malcolm soon finds himself under the coach's skin due to his constant complaining, which eventually gets him kicked off the team. Determined to put an end to his horrible habit of talking before he thinks, Malcolm starts "holding his tongue" which solves all the problems with his coach, girlfriend, and parents, but it ends up causing more stress than before. Meanwhile, Hal takes up speed walking and is desperate to be the best while Reese gets Craig to take him and Allison to a concert and almost ruins his date.
On a visit to Francis' dude ranch Hal can't help being disappointed in Francis' success, Reese and Malcolm fear Francis has turned into an overly responsible grownup, and Gretchen punishes Dewey for breaking a valuable doll.
Grandma Ida is even nastier than usual (if that's possible) because of a tumble down the front steps that resulted in a broken collarbone, prompting her to sue her daughter and son-in-law for pain and suffering. And there's more momentous news on the home front: Lois is pregnant.
After being rattled by a battle among the boys, a pregnant Lois ponders the consequences of raising another brawling kid. So she fantasizes that her unruly sons have morphed into well-behaved young daughters. Malcolm becomes Mallory, Reese is transformed into Renee and Dewey turns into Daisy.
A sex lecture from Lois rattles Malcolm; a ranch calamity unnerves Francis; disharmony among Hal's music group is a prelude to their concert. Also, a day in jail tests a defiant Reese, who faces a "Scared Straight" encounter.
After Lois is out of town, Malcolm and Hal got into a fight leading Malcolm to get expelled from his house. Malcolm lives with his girlfriend in her attic, as Hal put signs for "Missing Malcolm."
Malcolm tries to emancipate Dabney from his overbearing mother while Hal invites his ne'er-do-well old buddy to the house. At the ranch, Francis is forced to share a room with Otto.
A garage sale that's entrusted to Reese (yikes!) yields treasures near and dear, like Hal's old radio transmitter, which he makes operational. And a PC dating back to 1976 that Malcolm plans to sell to Craig for $1300.
An academic competition faces the Krelboynes in an event Malcolm derides. Especially when he learns his teacher has a cheating plan. Also: a commitment to a formal dance ruffles Reese, who's now trying to ditch his date.
Hal and Lois are penning their will, and think back to all the trouble their sons put them through. It is there that Lois' problems with Francis are finally revealed and how her inability to admit when she is wrong lead to a lot of the problems the family has been dealing with.
When Hal and Lois go out of town for a "last chance" getaway before the baby comes, Reese has a big bash that gets out of hand. College-age thugs show up, cancel the party and set up a drug-making operation in the garage. All Reese and Malcolm can do is knuckle under. The good news is, Dewey's not around. The bad news is, his baby sitter is Lois's annoying co-worker Craig. Meanwhile, Hal and his very pregnant wife are off at a romantic retreat---feuding.
Leonard, a cynical, genius chess player with no friends or job, makes Malcolm think he could grow into a similar adulthood. Determined to prevent this undesirable fate, Malcolm tries to help Leonard change his life by lining him up for a job interview with the obnoxious Craig. Meanwhile, Francis finds employ as a nude model and begins to delight in the exposure.
Lois goes into labor while Hal and the boys are at a bridal exposition. Ida moves in after her apartment burns down and she refuses to stay with Susan.Dewey reveals the date his parents chose for the baby's planned delivery is his birthday in an announcement at the exposition to humiliate Hal.
When Dewey's pet rabbit does good in a state contest, the family must travel to Las Vegas for the nationals. But Reese unknowingly sells the rabbit to a restaurant. Now it is up to Dewey (with a little help from a "choking" Reese) to try and save the rabbit.
Meanwhile, Malcolm tells Hal and Lois that they embarras him, and that is why he didn't tell them he won state science honors. As a form of repayment, Malcolm gets great seats for him and Lois to see Lois' favorite singer. Lois then gets lucky and is invited backstage where all she really wants to do is figure out why Malcolm doesn't want her around.
Hal, on the other hand, is looking all across Las Vegas for a slot machine that he has had dreams of winning the jackpot on.
Francis is also in trouble when he gets behind on duties at the ranch, and for the first time sees that Otto isn't just a pushover for everything.
Hal and the boys offer to watch baby Jamie so an exhausted Lois can finally get some sleep. Hal leaves the boys in charge while he goes to the Lucky Aid to pick up more diapers. While the boys are watching Jamie, three beautiful teenage girls arrive and woo Malcolm, Reese and Stevie away for the night, leaving Dewey alone with the baby. Meanwhile at the Lucky Aid, Hal doesn't have enough money for the diapers and Craig forces him to work. Back at home, Dewey concocts an elaborate bedtime story for Jamie involving each member of his family.
Malcolm gets a job working for Lois on the drugstore loading dock but is shocked to find that Lois smokes. She makes him promise not to tell, then turns her back on him and writes him up for a silly offense. Meanwhile, Dewey runs away to the Ranch to be with Francis because he says he is tired of Reese and Malcolm. Hal is also busy, secretly betting on and entering Jaime in baby competitions.
Hal, Reese, Malcolm, and Dewey go into business selling Christmas trees, with the boys using some of their own money, but two priests send homeless people to their business, trying to sabotage their sale.
Neighbors have the annual "The Wilkersons are gone" block party until they come home early. Reese and Dewey set up a plan to get money by letting Reese-tortured kids get revenge. Hal and Lois enter a kielbasa-eating contest and Malcolm unknowingly assists a robbery, but a surprising twist comes in the end.
Malcolm alerts the A.C.L.U. when he encounters censorship working on the high-school literary magazine; Hal tries to flirt with the woman in his office responsible for cutbacks.
Jamie's babysitter coerces Malcolm into doing a "small" task for her; Dewey finds a friend, only to lose him to Reese; Francis persuades Otto to confront an old adversary that once courted Gretchen.
Malcolm gets his tongue pierced and needs to hide it for a month. While Lois' mother, Ida, comes and annouces that she will marry a rich Chinese Man that she met on a cruise. Malcolm gets complications when his tongue ring gets infected, rendering him unable to say "S's" and he discovers that Ida has been drugging her fiancé with opiates and mood enhancers. When Lois and Hal confront Ida, she drugs them with free food. But luckily, the fiancé misses a drug treatment, and realizes that Ida is a terrible woman and he leaves her at the altar. Malcolm is punished for his tongue piercing. Meanwhile at the ranch, Otto decides to hire a murder mystery acting troup, but it all turns out badly.
Malcolm is convinced to play Softball by Lois and ends up doing very badly at it due to Lois's hold on him. Meanwhile, Francis tries to pick fights with Lois, Reese tries to break Francis's record of collecting toilet seats from a local junkyard, and Hal accidentally applies to become a member of the CIA.
Lois' younger sister, Susan, pays the family a visit and brings with her expensive gifts for the boys, biting remarks for Lois and a cold shoulder for Hal – whom she has never forgiven for dumping her for Lois. Lois and Susan's competitive relationship takes a turn for the worse when Susan gives Malcolm and Reese her prize '65 Mustang convertible. But when Lois discovers that Susan needs a kidney transplant, she puts her anger aside and offers to donate her kidney to Susan, which Susan only sees as the perfect opportunity for Lois to one-up her.
Lois blows her top over a hidden 15 percent surcharge on the bill at her family's favorite pizza place and stages a boycott...but Hal and the boys are sneaking slices on the side. Malcolm meets Angela and becomes instantly smitten with her intellectual family...but starts to feel like a heel because he's asked another girl to the school dance and is forced to break it off with her--er--them. And Francis is reluctant to let Otto hire an assistant for him...but soon comes to like the idea.
Lois tags along with Malcolm as he visits a college, but she's determined to room in the dorm Malcolm is staying in when she learns the room is co-ed. Meanwhile, after his father denies him a piano, Dewey begins stealing objects from around the house to amuse himself and to drive Hal crazy. Reese meets a girl, who he thinks is a narc, and he pretends he is a dealer, unaware that she is really an undercover cop.
Hal sets up Abe Kenarben on a blind date with Jaime's babysitter Polly but then realizes Lois has also set her up on a blind date - with Craig. Malcolm, Dewey (with his "lucky" shirt) and Reese also meet Reggie Jackson and Francis is embarrassed by Piama in front of his co-workers.
Malcolm convinces Dewey to do poorly on an I.Q. test, so that he won't become a ridiculed Krelboyne student. But Dewey does so badly that he is placed in a class for the emotionally disturbed. Hal and Craig compete in a dance competition.
When Dewey's annual candy selling event for school comes up, he uses the excuse of "these bars help support america" to sell them. Malcolm and Stevie attempt a science experiment, and are shocked when Reese begs to help.
Reese's new girlfriend Beth is about as dumb as he is. Malcolm initially dislikes her but they soon get to like each other too much and Beth breaks up with Reese. Devastated, Reese runs away and joins the army under the false surname.
Reese continues to be a great soldier in the Army until he finds himself in a situation where his Sergeant cannot help. But after comparing being captured to being grounded, he takes action and leads his team to victory. But being such a successful soldier has it's bad parts as well, as Reese prepares to jump from the plane - right into Afghanistan. Malcolm has his hands full as well as he attempts to prove Hal innocent. But being good with numbers helps as Malcolm notices all of the prosecutions given dates are on Fridays - which Hal hasn't worked on in over 15 years. And with Reese missing and Hal's case, Lois falls deeper and deeper into insanity.
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.
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!
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.
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 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.
