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- 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.
- Having been denied a very lucrative job in a software company, Malcolm accepts the vision his parents have for him. The first US president that will actually keep in mind the best interests of poor people like his own family.
- Malcolm and his family goes to Hals father's house for a reunion. The family doesn't like Lois. Reese and Dewey try to get in their grandfathers will. Malcolm's grandfather takes a special interest in him, while the young cousins love Francis.
- After Reese is severely humiliated by four girls at school, Lois exacts revenge on them; and Hal builds a pitching machine while hiding out from Lois in the garage.
- Lois fantasies what her life would be like if she'd had girls instead of boys.
- Malcolm sucks at street-hockey, frankly because he has no skates. So he turns to his father, who trains all his sons in the secrets of skating before he allows them to have their own pair. Neither of his bigger brother tell him about his fathers training and Malcolm gets even more anxious as Hal gets very mysterious about it all, but nothing can prepare either one of them for what is to come. Lois hurt her back terribly and has to stay in bed, which does not keep her from tyrannizing Reese and constantly trying to avoid being drugged with pain medication by her loving husband Hal. At the military academy everybody is preparing for a weekend of survival training without any comfort, except for Francis who tries to ditch his comrades.
- The family takes a day vacation at the water-park. All except Dewey, who has to stay home with an overage babysitter, which turns out to be more fun than expected. While Malcolm and Reese get into a loop of revenge-pranks, Hal and Lois try to enjoy the day off. As Dewey's babysitter hits the dance-floor, in more than one way, the youngest member of the family sets off on his own.
- 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.
- 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.
- When Lois finds her red anniversary dress burnt and in the toilet, she immediately suspects Reese, Dewey and Malcolm of foul play, and chases them all over the house to try and make them fess up, while Hal waits all night at the restaurant alone.
- 2000–200622mTV-PG8.4 (769)TV EpisodeHal's trial continues as the evidence pointing against him grows; Meanwhile, at training camp, Reese and his team are captured by enemies because of Reese.
- The family joins the Burning Man Festival, where Reese and Lois find creative freedom, Malcolm finds love, Hal finds a big audience and Dewey find himself doing all the chores.
- 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 have to go to the Krelboyne class picnic. Malcolm doesn't want to go because he has to do an act and doesn't want to look bad in front of his family especially Francis who is home for the weekend. Francis promises to get Malcolm out of doing his act but meets a girl at the picnic and no longer wants to leave. Lois tries to fit in with the other parents unsuccessfully and Hal serves meat from the BBQ even though the Krelboynes all voted that there would be no meat. Reese ends up on the run from eraserheads brother who catches him in the end giving him a wedgie. When Stevie leaves his chemicals with Malcolm, Malcolm desperate to do anything to get out of his act tries to make a stink bomb but ends up making a level 3 toxic bomb. The picnic seems to be ruined until Malcolm guiltily goes up on stage to preform his act. Everyone is amazed by it especially his family. Malcolm fears they will all treat him differently but to his relief nothing has changed.
- 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.
- 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.
- Reese goes on a high-speed car chase during drivers'-ed class.
- When Lois comes out of the store and catches the boys vandalizing a suggestive billboard from a strip club, Malcolm decides to challenge her by changing the display to "I Want Respect", thus starting a protest against it. Everyone in the lot believes them and follows the ruse. However, Lois doesn't believe them and thinks they're just being hooligans as usual.
- 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.
- When his parents fight over a new bed, Dewey writes an opera based on their arguments; Malcolm gets into "street luging" and becomes obsessed with beating a cocky rival, unaware the talented competitor is Stevie; and Jamie has his first crush on a baby he sees through the window.
- 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.
- Malcolm has been labeled a boy genius and is moved, much to his chagrin, into the Krelboyne class, which is a class full of nerds and geniuses like himself.
- 2000–200622mTV-PG8.2 (745)TV EpisodeWhen Reese's girlfriend Beth cheats on him with Malcolm, he runs away to join the army; Meanwhile, Hal is arrested for supposedly hatching out an entire criminal scheme at his job.
- It's another family Thanksgiving, as Reese cons Hal and Dewey into helping him out with the cooking. Francis and Piama are also there, but they're not even speaking to each other. Lois tries to intervene, but it goes nowhere, as Hal prevents her from intervening. Soon after, all the family members start arguing with each other, claiming that this is the worst Thanksgiving ever. Meanwhile, Kirsten has invited Malcolm to her house party. He's having a blast without his family dragging him down and calls it the best Thanksgiving he's ever had in his life.
- When Lois is arrested for having 16 unpaid parking tickets, she makes Francis pay for them and fights the cop in court for falsely accusing her of something she never did.
- Trying to bury the fruits of their mischief--one of their father's trophies in the backyard--Reese and Dewey find an old bunker, in which they trap Hal to avoid punishment. Malcolm and Lois are in a competitive mood. Malcolm discovers his talent to dance, which he takes to a dance competition with Danielle (Lynsey Bartilson) and Lois keeps hold on a car until the bitter end.
- One fish, two kobe steaks, three girls, four sub-plots, and five brothers come together for an evening at home when the power goes out.
- Malcolm, Reese and Dewey "volunteer" to do charity work at the local church. They soon begin bartering the many items in the church basement in exchange for money, but when the boys start making more of a profit than the church, their consciences finally catch up to them. Meanwhile, arriving in Alaska to begin working with his former classmate, Eric, Francis learns quickly that his great expectations are more like a wilderness nightmare, and his new boss, Lavernia, may be the icing on the tundra.
- 2000–200623mTV-PG8.1 (1.1K)TV EpisodeWhen Francis shows up a week late for Halloween, he and the boys still manage to create the ultimate prank; Hal tries to catch a man who keeps speeding down the street, which leads to Lois and him stealing the car.
- Jessica teaches Malcolm how to manipulate Lois, Reese prepares to mail himself to China, and Hal is terrorized by a bee.
- 2000–200623mTV-PG8.1 (859)TV EpisodeMalcolm is fed up with the fact that every time he complains, something wrong happens. He has recently got kicked off the basketball team and vows not to complain anymore. He receives good results by not complaining - he gets back on the team, negates Lois' anger by not talking back to her, and gains the respect of his girlfriend, Nicki, who shares a kiss with him. Next, Hal decides to be a speed waker and soon gets competitive with a local walker. Meanwhile, Reese wants to take Alison to a concert and the only driver he can find is Craig Feldspar. However, Craig has plans of his own for his two passengers - a hay ride and a bonfire dinner. Alison is fed up and pepper sprays him and threatens to give Reese the same treatment if he doesn't let her go her own way. He's pissed off as Craig plays his ukulele and sings a song from Air Supply.
- Francis makes Reese and Malcolm fight each other and suck up to him for wrestling tickets. In the meantime Dewey takes care of Craig's cat Jellybean while he is gone to a comic convention.
- Neighbor Jessica stays at the house, and pulls a prank on Malcolm and Reese convincing each of them that the other is gay; Meanwhile, Hal battles a neighbor in Christmas decorating.
- 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.
- It's another Wilkerson family Christmas- Reese, Dewey and Malcolm misbehave a time too many, so Lois moves the tree and all the presents to the garage, which she called, "holding Christmas hostage". While Francis, much to his chagrin, goes to Canada to visit Grandma Ida, whose Christmas spirit was running on empty. Much like her gin bottles.
- Malcolm and his family go to Hal's work picnic. Hal tries to avoid meeting the new boss and in return is mistaken for the boss. Dewey eats too much candy. Malcolm meets up with a girl from his past. In Alaska, Francis goes up against a girls ice hockey team in order to earn some much needed cash.
- 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.
- 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.
- Aunt Helen died and the family prepares for the funeral, an occasion that doesn't go as planned. Dewey finds a stray kid, Malcolm tries to avoid going altogether, Reese tries to sink some Evidence with aunt Helen's casket, Francis tries to get involved more into family matters, Hal prepares a speech, Dewey tries to get his new friend Egg home and Lois is all about family obligations. Of course it turns out much different then anybody anticipates.
- Craig hires an evil helper monkey. Reese catches a burglar and decides that he would like to try being in law enforcement. Francis and Piama are forced to leave Alaska.
- Malcolm stays overnight at Stevie's house. He convinces Stevie to sneak out of the house with him and they go to an arcade downtown, but Stevie's wheelchair is stolen, and they have to team up to find his wheelchair while dragging Stevie in a cart. Meanwhile, to prove that he is mature, Lois challenges Reese to give Dewey a bath and put him to sleep in exchange for being allowed to stay up late to watch a scary movie, but the task proves more difficult than he expected, just as Lois thought it would. At the academy, Francis is hazed by a group of students, but tells them their tricks are amateurish to what Lois did to him, and the students decide to worship Lois.
- The boys were grounded for a while for losing Dewey's bike and can't wait for their release, but Lois is sick in bed and mistakes Monday for Sunday. But the boys appreciate the opportunity to ditch school. A letter from the academy arrives, which would cause some trouble for Francis and the boys decide to hide it, until they find out that it was Francis that sold them out about the bike. While the boys turn against Francis, Hal is at a Porsche shop and gets tempted to buy a car he can not possibly afford.
- Francis is home to repair the roof, while Reese has even more troubles with his grades than 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.
- Reese and his partner from the scavenger hunt cause problems. Malcolm gets into trouble with a girl. Hal finally meets his new boss. Francis decides to cheat in the ice hockey match in order to win money. Dewey is on a sugar high.
- Hal takes the boys to a bridal show; Lois' mother wants to move in with the family; Malcolm gets an offer to enroll in a prestigious private school.
- Lois continues with her strenuous labor, as friends and family all panic around her.
- 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.
- While we have a chance to see the world from Dewey's very special point of view, Reese acts weird. As it turns out, he is interested in a girl and does not know how to show her how he feels. Following a misunderstood advice from Malcolm, Reese joins the cheerleader-squad. As a consequence Hal has to have "the talk" with his sons. Meanwhile in the military academy Francis gets to know Commandant Spangler on a very personal level.
- Upon coming home from school, Dewey adopts a dog named Marshmellow and decides to hold Malcolm and Reese hostage for all the things they did to him while he was growing up.
- 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.
- Strapped for cash for the holidays, Hal and Lois decide that all Christmas gifts this year should be handmade. But when Hal sees the thoughtful, quality gifts the boys made, he feels bad about his shoddy attempt and panics.
- Reese and Malcolm find out that there was a murder in the family's house before they moved in. Hal is highly agitated in fear of ghosts from the murder and Malcolm tries to reason him out of it. Meanwhile Reese and Dewey take Jamie Trick or Treating and make a persistent enemy, whereas Lois is stuck at work because of a shoplifter no one want to take care of.
- Dewey tries to prove he can take responsibility by taking care of the class hamster for the weekend, his efforts being ignored by his parents who secretly try to wait out possible bad news from Hal's doctor. Meanwhile Reese and Malcolm try to ditch home for a party and Francis has to fight Lavernia, his boss.
- While Hal and Lois are away for the weekend, Francis, visiting home from military school, is in charge of the house. Right away his friends come over and mess it up, so Francis and the boys clean it up to show Francis is responsible and might be allowed to leave military school and come home. All goes well...until a shelf falls on Malcolm, injuring him.
- Because of Dewey always leaving food in the crawlspace under the house, the whole family is forced to live in a trailer owned by Lois' coworker, Craig, while their house is being fumigated. However, Malcolm ends up spending more time at the home of an upper-middle-class family who has hired him as their babysitter, but he learns that they were secretly videotaping him. He later blackmails the family to leave him alone and quits the job, also revealing a horrible secret about the family's wife. Meanwhile at the academy, Francis finds the corpse of a former janitor in the basement of the military school, who was missing for 16 years, and teams up with his friends to give the forgotten custodian a proper burial by sending him down the lake in a burned boat and performing a burial at sea, which turns into a disaster.
- Lois has a dispute with Hal and the boys' favorite restaurant; Malcolm clicks with his girlfriend's family to the point where he forgets about his girlfriend; and Francis gets an assistant who tends to his every whim.
- After being invited to a game of poker by Abe, Hal is disappointed as the game turns out to be completely different from his expectations.
- Hal lands a second job at an electronics store, while Malcolm is dumbfounded by their new babysitter, who's the same age as himself.
- Malcolm realizes the entire neighborhood has been throwing a block party when the family leaves town for an annual vacation; Hal and Lois participate in a kielbasa-eating contest; neighborhood kids pay money for a chance at beating up Reese; and Otto acquires a device for "extracting seed" from a bull.
- 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.
- Lois finally gets Dewey out of the Buseys special needs class. In response to losing their new 'leader' they run away to be with him. Hal still has no job and picks up a bunch of dumb, but nice, body builders for his latest manic craze.
- The family decides to hold a garage sale to fund repairs of the bedroom wall and Lois puts Reese in charge. Hal finds his old radio-transmitter and starts running a pirate broadcast like he once operated in college.
- When Lois' mother visits, she trips on a leaf and decides to sue Hal and Lois...just as Lois finds out she's pregnant again.
- Waiting in Lucky Aide for Lois to end her shift, Reese and Malcolm cause trouble, which leaves Dewey unobserved and able to nick something expensive from the store. Lois tries to make a point about "doing the right thing" and loses her job in the process. It also leaves the family with less income, bad food and Malcolm stressed out, especially because he already is in emotional despair over Julie Houlerman. Malcolm gets caught in an awkward social situation and Lois struggles between standing up to the man and providing for her family. Meanwhile Francis gets a break from the academy as honor guard for a beauty pageant. Every cadets dream come true?
- Reese is kicked out of home and soon discovers how expensive it is to rent an apartment. Meanwhile, Malcolm helps a football player apply for college.
- Lois returns to work at the market as a probationary employee and takes offense at the racist advertising standee for malt liquor. She hopes Malcolm will see her point of view but he is resistant and this leads to a battle of wills between the two. Hal is involved in another battle of wills; this one with the garbage man.
- Lois takes off to visit Francis at the academy, which might make his recent appendectomy just a little more painful. Without Lois, Hal devolves to his former bad boy personality, which turns the robot Malcolm builds with his Krelboyne colleagues into a much more destructive power than expected.
- The family goes to the zoo. Malcolm is going through a crisis, and he and Dewey find themselves in a unfortunate situation. Reese angers an animal at the zoo. Hal is jealous of a former flame of Lois's who works at the zoo.
- The boys and Stevie take off in the evening to visit the carnival but get into trouble, while the parents go searching for them.
- Hal and the boys enter the season of goodwill in a competitive spirit when the local church starts to undercut them on Christmas tree prices.
- Malcolm and the rest of the Krelboynes are forced to re-join the rest of the school with disastrous results. Dewey is stuck at home with chicken pox and builds a dominoes masterpiece, which Hal wants to knock down.
- Malcolm is shocked when he finds a major difference in Cynthia's physical appearance after her semester in Europe, and tries to save her from being the victim of Reese's selfish, evil plan after he accidently finds out.
- When Dewey is in danger of joining the Krelboynes, Malcolm interferes with disastrous results. Meanwhile Hal 'discovers' his latest mania when he sees Craig dancing in a family restaurant.
- Reese inadvertently perfects Malcolm and Stevie's science experiment, but can't remember how he did it; Dewey dreams up reasons for people to buy the candy he's selling door-to-door; and Francis aids a piglet.
- Malcolm sneaks around to date a girl whose father hates him; Hal and Lois become more productive when they can't have sex for a week; Dewey discovers he's an "evil twin"; Francis mediates a dispute between Otto and his cowboy neighbors.
- Stevie goes into shock when he's told Kitty divorced Abe; Reese gets caught up in the hot-and-heavy entries in a diary, unaware it belongs to Lois; Otto and Francis have to put down an old horse; Dewey finds he likes the taste of baby food.
- 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.
- Hal is stressed about a gift for Lois for their 20th anniversary. He begins sleepwalking, and Reese discovers Hal is highly suggestible in that state. Meanwhile, two of Dewey's Busey classmates run for student council.
- It's Hal's birthday and Lois has Francis come home to celebrate it with the family as a surprise. The surprise is on her and the rest of the family as Francis comes home with a wife he married in Alaska named Piama.
- Hal feels betrayed when his friend Trey charges $2,000 to fix Hal's tooth; Malcolm and Dewey find a new mattress; and Reese teaches Lois how to ride a bike.
- Having forgotten to pay the bill for the family's health insurance, Hal tries to protect the boys from all accidents for the weekend; meanwhile, Lois accidentally gets Craig into trouble with their co-workers.
- 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.
- In a desperate attempt to get rid of his Krelboyne past and start afresh, Malcolm ends up making things even worse than they were.
- Lois is completely mortified when she is called slovenly at work and is asked to dress up her appearance.
- Lois uses a long drive with Malcolm to further his sex education; Reese spends a day in prison; Dewey plants seeds of discontent in Hal's vocal group; Francis has an accident branding Otto's favorite cow.
- Lois gets Malcolm a job at the store, exposing Lois's well-kept secret; Hal and some other fathers start betting on babies; and sick of the way his brothers treat him, Dewey travels to the farm to visit Francis.
- 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 ?
- The neighborhood dog pack adopts Reese as their new best friend, and Dewey gets caught after spending time with a new, better mom. Hal becomes the company's motivational guru.
- Francis shows up for his 21st birthday anticipating Hal will come through on a promise to go on a motorcycle road trip; meanwhile, the boys are trapped in the house while a bully waits outside.
- Hal has his friends over to his house for their poker game, and tries to impress them in the process. Reese convinces two girls that Stevie has a fatal illness. Malcolm discover something dangerous in the house. Dewey has no place to go.
- Hal takes the day off and the boys to the stock car races, while Francis gets into trouble with Commandant Spangler which leads to troubles with his fellow cadets, but that can not stop Francis from aiming for the next big possibility to screw up - this time it involves a Dog and a Snake. As Lois is searching for a check, she discovers more and more dirt on each family-member, hidden in the dustiest corners of the house, which she piles up for later use. Meanwhile the boys get bored at the tracks fast and get into problems on their own.
- 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.
- 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.
- When an exhausted Lois falls asleep, Hal goes out for diapers, only to be branded a shoplifter; three beautiful girls use Malcolm, Reese, and Stevie to embarrass their prom dates; Dewey tells the baby a fantastic tale to keep him from crying.
- While Lois and Malcolm are laid up with mono, Hal discovers another side to the neighborhood; meanwhile, Dewey tries to introduce Reese to kinder, gentler ways of dealing with Jamie.
- In a desperate bid to get to Alaska, Francis unintentionally ends up blowing things way out of proportion by landing himself in a sticky situation.
- In a bid to get to catch the flight to St. Louis for Dewey's piano competition, everything seems to be going wrong for him. Meanwhile, Reese and Malcolm compete with each other to see whether Reese is man enough for the likes of Ida.
- It's Spring break, and Malcolm is stuck working the graveyard shift with his mom, and Reese inherits a box of caterpillars from a shady pest controller. Malcolm investigates something weird at work.
- Dewey invites a destructive friend for an overnight visit; Lois is on the hunt for a decade old blender warranty.
- When Malcolm becomes editor of the high school literary magazine, the principal instructs him to censor a well-written story; Lois encourages Hal to flirt with a new supervisor so he can keep his job; Francis teaches Otto how to waltz; and Reese pulls a prank on Dewey.
- Today is Malcolm's birthday and unfortunately he and Reese are in a long prank war against each other. Meanwhile Francis does battle with a legend about an evil cow at the Grotto Ranch and Hal is forced to enlist Craig Feldspar to help him with a comic book present.
- When Grandma Ida visits the family once more, she ends up saving Dewey's life from being run over thus having her leg amputated. Lois forces Francis to take care of his grandma as he's unemployed. Meanwhile Reese and Malcolm decides to go three days without sleeping on the grounds that one of them will be super glued if he fall asleep. Dewey tries to have a leg funeral after feeling bad about what happened to Ida.
- Grandma Ida makes another conjugal visit at the Wilkerson house. This time she isn't alone as she walks in with her beau, Mr. Li a wealthy, widowed Chinese man whom she met at a cruise. Hal and the boys see this as an opportunity to get Ida off their backs once and for all. But Lois thinks that her mother is up to no good as usual. Meanwhile, Malcolm has just got his tongue pierced, but it gets infected right away so he can't say any words that involves an "s" in them. On the day of his grandmother's wedding, he confirms his mother's suspicions when he finds anti-depressant pills in Ida's bag.
- Ida forces Lois to bake a special tart for an old-world saint's holiday; Malcolm meets his match with music appreciation; and Hal tries to bond with Reese by watching gory horror movies with him.
- Lois' younger sister, Susan, makes a surprise visit to the Wilkerson house. Immediately, she treats Malcolm, Reese, and Dewey like the sons she wishes she had with Hal instead of being single and alone. She also treats Lois as a plague in her life and blames her for being unmarried status. She tells the boys that ever since she caught their mother having sex with their father, she has refused to accept their relationship. However, Susan is plagued with a kidney disease and Lois tries to offer hers for her sister.
- When Malcolm's arch nemesis and former teacher, Mr. Herkabe, crosses the line and hurts Reese's feelings too many times, he decides to pay him back for hurting his brother by revealing his former teacher's awful secret. He had flunked gym and lied about it. Because of that truth, the Principal decides to strip him of his trophy and hand it back to the one who passed gym, despite her blindness. Meanwhile, Hal gives Dewey a ton of wrong advices to a girl he likes.
- Malcolm's teacher forces him to secretly record Reese as he divulges his innermost secrets; Francis strikes back after a critic writes a scathing review about the hotel; Dewey starts his own novelty act at an outdoor mall; Hal's bosses are placed under arrest.
- The boys, in an effort to prank their mother, enroll Lois in the Tri-County Mom Pageant, with Hal as her coach.
- Reese, having deserted the army is trying to find his way home. Lois discovers his fate and goes in search - eventually to the Middle East. After cornering him with the help of some locals he is dragged 'all the way' back home by his ear. Meanwhile Malcolm and Dewey try to honor his probable death by doing something Reese would do.
- Reese lands a part time job at Circus Burger, which seems like a good job. Until he meets his supervisor, Francis' dim-witted friend Richie, who, along with his co-worker cohorts, set Reese up as a patsy.
- 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 involved in complicated relationships with the hottest girl in school and Jessica. Lois worries about what Reese will be doing in the future.
- Malcolm finds himself being antagonized by a new bully, Kevin. This kid was always mocking him, teasing him, at lunch he cut right in front of him. On pizza day! But after Kevin taunted him about it one time too many, Malcolm loses it and attacks the kid, but deeply regrets it after learning his bully was 7-years-old; Hal cuts down the huge tree in the front yard, and he and the boys have just a little too much fun with the wood chipper.
- Malcolm stops thinking in order to go out with a very dumb girl. Hal wins some money, and rents a steamroller.
- 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.
- Hal's father dies, but he fails to show emotion for his departed father, which leads him to wonder whether his children would miss him when he dies.
- Malcolm decides to organise a "Morp", an alternative to the traditional Prom, for those pupils shunned by the "cool" kids. Meanwhile, Reese agrees to hire himself out as an escort for the evening.
- Dewey and Hal attempt to quit their vices, Reese threatens Stevie, and Lois opens up to Jamie.
- Malcolm competes in an academic octathlon but hates the intensity of the other competitors; Hal fights to regain Dewey's love; Reese tries to get out of going to a formal dance; Francis and Piama's argument over chores proves highly contagious to other couples.
- Reese is visited by an Army buddy who develops a crush on Lois. Hal starts feeling useless when Lois buys orthotics and no longer needs his tender loving care.
- Unable to function without Dewey, Buseys special needs class panics and takes their teacher hostage when he threatens to call the police on one of the kids for a minor infraction. After other faculty members are taken, a return visit from Dewey accompanied by Francis leads to a new revelation about the "education" the kids are receiving.
- Raduca whips Reese into shape while pursuing her own interests; Dewey visits unemployed Francis; Hal discovers the benefits from taking on Malcolm's college interviewers.
- Malcolm meets a chess-playing bum who could be him in 30 years; Lois can't figure out why she's gaining weight; Dewey attributes his bizarre behavior to obeying requests from the fetus Lois is carrying; Francis objects to Piama posing nude in an art class.
- Hal spends a wild night with an old high school buddy; Malcolm tries to liberate Dabney from his mother's control; Francis spends the night with Otto when their wives are out of town.
- Lois finds an amazing and cheap massage table at the grocery store and manages to become so relaxed that she doesn't even care about Hal and Dewey's LEGO city.
- Lois and Hal clash after Hal purchases a hot tub; Malcolm gets his driver's permit, only to get mixed up in a dispute between Polly and her ex-boyfriend; and Reese steals Dewey's friend.
- When Hal kicks Malcolm out of the house for misbehaving, Reese tries to take advantage of Hal's distraction to come up with a truly bad stunt of his own, and Francis takes offense when Otto's musician nephew plays a musical accompaniment to Francis' every move.
- Lois accompanies Malcolm to his first college visit, where she clashes with a resident advisor; Reese pretends he's a drug user to woo a pretty narcotics officer; Francis and Otto open their own childcare center; and Dewey constructs his own musical instrument.
- Malcolm uses his illegal gambling profits to buy a junk car, which quickly takes over his life; Hal discovers a talent for hair styling; and Lois discovers Craig is having an affair with the boss' wife.
- Malcolm gets his first official girlfriend; Dewey hijacks his new friend's birthday party to better himself.
- While Malcolm battles a yearbook photographer to get a good photo, Hal, Lois, and Dewey intercept a scholarship check addressed to Malcolm and try to rationalize spending the money; Reese goes back to work delivering meat.
- Malcolm accidentally hits a ball into grouchy old Mrs. Griffin's yard, and when he goes to retrieve it, he has a run-in with the elderly lady that accidentally makes her fall and break her arm. As punishment, he must go over to her house every day after school to help her out. Meanwhile, Dewey begins to carry a purse to school instead of a backpack; and Francis must deal with his screw-up friend Richie at military school.
- When Hal and Lois go on a less-than-romantic getaway, Reese throws a party at home, which is crashed by delinquent friends of Francis, who take over the garage and hold the boys hostage.
- The family travels to Las Vegas when Hal experiences a dream about hitting the jackpot; Dewey and Reese enter an enormously obese rabbit in a contest; Lois gets to meet her favorite singer backstage; Otto and Francis get trapped in a well.
- Lois has just found out that she has a half-sister named Roberta and brings Reese, Jamie and Malcolm with her to meet their aunt and cousins. Her step-mother, Sylvia comments that she looks exactly like Victor and gives her a warm welcome. Despite some nervous moments between them, they're getting along great. Lois thinks it's going to be nice, quality time with them until a furious and vengeful, Ida arrives at the house to spoil everything. She has lost the court case and demands for Victor's pension from his secret family. Meanwhile Hal and Dewey plan to go racing together, but things don't go as great as they'd expected.
- Malcolm's afraid to visit his best friend Stevie in the hospital; Reese becomes a master telemarketer; and someone secretly tries to drive Lois crazy.
- Francis has made it through a year of sobriety and he invites the family to his AA meeting, until Lois discovers that he has invited her there to place his problems on her.
- Trying to win a battle of wills with young Jamie, Lois brings Francis home to help her remember how she conquered him when he was a baby; and Malcolm, Reese, and Dewey struggle to dream up a fun use for an old diving board.
- The family joins a church in order to take advantage of the free day care; Francis concocts a UFO story to help the dude ranch.
- Francis bails from military school in a desperate attempt to visit his stupid girlfriend.
- Hal has finally made a deal with Ed for the boys to have their own computer. Unfortunately, it doesn't come without favors. They find out that Ed is a philanderer and has a ton of undeleted e-mails from the women in their neighborhood to prove it. Reese sees this as an opportunity to blackmail him to his own twisted scheme. Then, Hal decides to coach Dewey's losing team into better soccer players. Meanwhile, Piama is fed up with Lavernia mistreating Francis, and decides to make her pay for it. She steals her precious parakeet and holds it hostage until Lavernia treats her husband better.
- Lois has to go on jury duty, and Hal tries to figure out what case she is on. Malcolm, Reese, Dewey, and Stevie go sewer pipe exploring. Francis goes ice fishing.
- Polly begins dating Abe and Craig; Malcolm refuses to believe in the power of Dewey's lucky shirt; the ranch hands make fun of Francis; and Lois takes the kids to a baseball convention.
- When Hal and Lois carve out some time for deep personal discussions, Hal is upset to learn Lois doesn't believe in an afterlife; Malcolm is roped into emceeing a silly charity auction at school, but can't help taking his responsibility seriously; and Reese feuds with Jamie.
- Malcolm gets promoted to a position promoting the Lucky Aide from atop a pair of stilts; Hal tries to make up for accidentally blowing the household budget on a phone-sex line; Dewey thinks Jamie has found a stash of Lois' jewelry hidden by Francis years ago; and Reese joins multiple drug studies.
- Hal has a hard decision on his hands, one of the neighbors has been in a coma and he has to decide whether or not to keep him on life support or pull the plug. He's always turned to Lois to make decisions for him. After another argument between the nurse and the doctor, he ends up paralyzed from the waist up. Meanwhile, Craig enlists Reese, Malcolm and Dewey to help him fight dirty against a childhood bully, who is indeed his estranged, healthy father.
- Malcolm volunteers for the company's softball team, only to realize that Lois is the coach; Francis sets out to prove he's not lazy; and Hal interviews for a job at a company that might be recruiting secret agents.
- Reese pretends to be a vegetarian; Hal decides to teach Dewey a lesson about the game of "Life"; and Malcolm talks Craig into standing up to Lois and then regrets it.
- Kitty returns to the her family after leaving them. However, Lois refuses to accept her back in the neighborhood and refuses to talk to her.
- As Lois and Hal write their wills in preparation for the baby's birth, they recall various colorful incidents with their four current children.
- Hal thinks that Malcolm, Reese and Dewey took a joyride and wrecked the cars, so he takes them to see a therapist.