Season 1

1. Pilot

Child prodigy Malcolm lives with his dysfunctional family: neurotic father Hal, controlling mother Lois, bully brother Reese, and odd younger brother Dewey. His eldest brother, Francis, resides at a military school in Alabama, Marlin Academy, for his misbehavior. At school, Malcolm tries to keep a low profile and avoid his bully, Spath, but his teachers spot his intelligence, and further testing reveals his I.Q. to be 165. Lois forces him to join the school's gifted class, but Malcolm objects because he doesn't want to be a "Krelboyne", a term for the gifted, socially awkward kids at his school. Frustrated due to being ostracized by the other kids, Malcolm lashes out at Spath, and, with help from his new handicapped friend Stevie ( Craig Lamar Traylor ), fortuitously humiliates Spath by making it seem like he pushed a wheelchair-bound Stevie to the floor.

2. Red Dress

Lois makes plan with Hal to meet at an expensive restaurant for their anniversary, but forgets to go after she finds the red dress she intended to wear burned and flushed down the toilet. She spends the night punishing the boys, trying to figure out which of them did it. Meanwhile, Hal makes friends with a member of the restaurant staff while waiting for Lois. Malcolm, seeing that he and his brothers cannot fight Lois alone, calls Francis for help against Lois, but this leads to further trouble for them when she finds out. Despite the tension, Lois decides to take the kids out to dinner, and Hal, coming home to an empty house, accidentally burns and flushes Lois' other dress, revealing he was the culprit.

3. Home Alone 4

While Hal and Lois are away for the weekend, Francis comes home from military school to babysit. Malcolm overhears a discussion between Lois and Hal's about Francis out of context, and believes he will be allowed to return home permanently if he watches over them well enough, so Malcolm convinces the other boys to be on their best behavior. A series of reckless behavior nevertheless occurs, but the boys manage to fix and hide all of them in time. Seeing the good work Francis has done, Hal and Lois send him back for military school, on account of how much they think his behavior has improved since going there.

4. Shame

Fed up with his bully, Kevin, Malcolm beats him up, but it turns out that Kevin is only a 7-year-old, something Malcolm learns after he beat him up. Malcolm feels guilty and tries to clear his conscience, but ultimately fails, especially after Hal accidentally beats up Kevin's 15-year-old brother. Concurrently, Dewey is injured while climbing a tree, so Hal cuts it down, but they soon miss the tree, and so Hal plants another. Francis decides to steal the slides for the military academy's vulgar sex education slideshow, but he finds some embarrassing slides of Commandant Spangler ( Daniel Von Bargen ) in his office, which he replaces with the original slides. However, Spangler realizes this, and instead shows the cadets embarrassing slides of Francis.

5. Malcolm Babysits

When bugs take over the house due to Dewey stashing old food inside the walls, 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, which he prefers to staying with his family, but he soon learns that the parents have been secretly videotaping him to judge his bad behavior. He later blackmails the family with evidence of their affairs and illegal practices to leave him alone, and he quits. Meanwhile, Francis finds the corpse of a missing janitor in the basement of Marlin Academy, and teams up with his friends to give him a Norse funeral, which goes wrong when the corpse blows up in a fiery explosion.

6. Sleepover

Malcolm spends the night at Stevie's, but finds his parents to be overbearing. After they are put to bed early, Malcolm convinces Stevie to sneak out to an arcade downtown. As they leave, they realize that Stevie's wheelchair has been stolen, and they look for it, tracking it down to two older teenagers, who run off and leave them the wheelchair. Meanwhile, to prove that he is mature, Lois challenges Reese to put Dewey to sleep in exchange for being allowed to watch a horror movie; the task proves more difficult than Reese expected, and ends with him falling asleep from exhaustion as Dewey watches the movie.

Francis is hazed by a group of upperclassmen, dubbed the "Brothers of the Apocalypse", who engage in cult-like behavior. When he is kidnapped, he tells them that their tricks are amateurish compared to Lois' behavior, and so the students decide to worship her and adopt her ways.

7. Francis Escapes

Francis deserts from Marlin Academy to reunite with his girlfriend, Bebe, and he hides out in the family's backyard, telling Malcolm not to tell them. However, Bebe breaks up with him as soon as they reunite, and Lois soon finds out that Francis has left school, but does not know where he went. Malcolm tries to keep it a secret, but Lois pushes him into tattling, causing her to go looking for Francis. After Hal finds him, he sympathetically decides to drive him across the country back to military school so Lois won't find him.

Meanwhile, the boys tell Dewey that there is a monster under his bed, scaring him; when he hears Malcolm talking to Francis in the backyard, Malcolm lies and says that he was speaking with the monster. After Bebe breaks up with him, Francis begins to cry, which Dewey mistakes for the monster's roar, and he unintentionally hurls rocks at his brother.

8. Krelboyne Picnic

The family spend the day at 'Cirque de Krelboyne', a picnic where Malcolm's classmates demonstrate their academic abilities, something Malcolm feels ashamed he has brought his brothers to. Hal violates the picnic's vegetarian policy by bringing a meat-filled cooler, giving the people food that they all spit out in disgust. Lois also starts a rivalry with a woman on the PTA who strictly oversees the food and drinks at the picnic, tossing out Lois' brownies. Reese looks forward to bullying and beating up the "Krelboynes", but is soon on the receiving end when one of them gets his older brother involved, who pins a remorseful Reese to a fence.

Despite Malcolm's attempts to escape, he is eventually forced to take the stage at the talent show, where he stuns the audience with his mathematical prowess. Concurrently, Francis meets another sibling, who soon becomes his girlfriend, but they break up immediately after an argument.

9. Lois vs. Evil

Lois finds out that Dewey stole a $150 bottle of cognac from the store she works at. She makes him return it, but finds that she has been fired by an assistant manager named Mr. Pinter who has been bullying Lois for her entire time there. This leaves the family struggling financially, especially when Hal eats peaches, a food he's allergic to, and they get back an expensive hospital bill. Lois gets her job back from Pinter when she confronts him for his own misbehavior, which all the other employees overhear, resulting in Pinter quitting. Concurrently, Francis, while volunteering at a beauty pageant, gains special backstage dressing room access when some of the contestants think he's gay. He tries to tell one of the contestants that he wants to become straight, and that she could help him, but she instead sends him to a Christian conversion camp.

10. Stock Car Races

Hal sneaks the boys out of school and takes them to a stock car race. Bored, the boys try to sneak on the pit lanes, causing them to be sent to the security guard's office, where they run off with Hal. At home, Lois' hunt for her lost paycheck unearths incriminating items that Hal and the kids have stashed around the house, while Malcolm's teacher comes over, sparking a friendship as she helps Lois look. Meanwhile, fed up with Spangler and his noisy dog that all the cadets hate, Francis sneaks a large snake named Otis into the academy and stashes it in his locker. The snake soon escapes and eats the dog, resulting in Spangler punishing all the cadets, but they are too excited about the dog being gone to care.

11. Funeral

The family prepares for their Aunt Helen's funeral, but, after Malcolm gives her a hard time arguing about skipping it to go to a concert with Julie (Landry Allbright), a girl he likes, Lois gives up and decides to take a bubble bath while everyone else does their own things. Hal listens to his old record player, while Dewey invites a friend—who he nicknames "Egg"—and after they leave a spill in the kitchen, they make a bigger mess trying to clean it. Julie comes to see Malcolm, but she catches him changing in his underwear and runs away, getting injured when slipping on the spill.

Malcolm takes Francis' advice to use a scapegoat, and tells his parents that Reese broke Dewey's birthday present and planned to stash the remains in Aunt Helen's coffin. Lois promptly decides that they will attend the funeral after all so Reese can apologize, and they attend it while he stands in the corner, punished.

12. Cheerleader

Reese joins the cheerleading squad to get closer to a girl he has a crush on; Malcolm is embarrassed to have a cheerleader brother, but he ends up helping Reese learn his routines anyway. Dewey desperately tries to talk Lois into buying him a new toy, and, upon getting it, decides to break it. Hal, seeing Reese cry and practice cheerleading routines with Malcolm, tries to give all the boys "the talk", but only upsets Reese more. After Francis gets in trouble, Spangler attempts to reach out to him by telling him a story of his youth, only for Francis to push Spangler into admitting he hates his mother, much like Francis does.

13. Rollerskates

Malcolm decides to take roller skating lessons from Hal, who enthusiastically takes it too seriously and is overly critical of Malcolm, leading Malcolm to yell "fuck you" at him. Meanwhile, Lois throws out her back by screaming too loud at Reese, and refuses to take painkillers, which Reese sneaks in her milk, leaving her unable both to scold the boys for their behavior, and to help Hal with his issue with Malcolm. At Marlin Academy, Francis fakes the same back injury to get out of a wilderness survival exercise at the academy, but is caught and thrown into the woods tied up with no supplies.

14. The Bots and the Bees

Lois visits Francis at military school after he has a medical emergency, and quickly gets along well with the rest of the academy, upsetting Francis. Hal, no longer under Lois' supervision, quickly regresses into his rambunctious teenage persona, resuming his smoking, refusing to show up to work, and letting Reese and Dewey get away with everything. Malcolm and the "Krelboynes" decide to enter a killer robot competition, but Hal takes over the project and builds a dangerous robot complete with a bee cannon, to the point that the boys are forced to launch the bees onto him so he'll return to normal.

15. Smunday

A sick, bedridden Lois does not realize she has spent two days in bed, and, assuming it is Sunday when it is actually Monday, does not make the boys go to school—or lift their latest grounding about giving away Dewey's bike. The boys are initially happy to get the day off school, but soon realize their mistake, as they cannot leave the house in case someone sees them and tells Lois. Francis calls the boys about hiding an incriminating letter home about his latest offense at the academy, but Lois ends up finding it anyway.

Caught up with both her flu and Francis' misdemeanor, she ignores punishing the boys for skipping school. Out of fear of Lois sending Francis to a prison farm, the boys try to come up with a prank that will make Lois divert her attention from Francis. Meanwhile, Hal visits a Porsche dealership and ends up ruining a car because he caught Lois' flu. The salesman drives Hal home in the car, where it is further damaged by the boys' prank.

16. Water Park

The family takes a trip to a water park, where Lois and Hal try to avoid the boys and have fun. Malcolm and Reese engage in an escalating war of pranks. After they spill Lois and Hal's food and drink, she berates them at the top of a large water slide. Malcolm pushes her in, but she grabs both of them they go down together as she still yells. Dewey, unable to go because of an ear infection, is left with a strict elderly babysitter, Mrs. White ( Bea Arthur ), who he bonds with, but she collapses and is taken away in an ambulance.

Dewey chases a blowing red balloon, and wanders off. Spangler learns that Francis has been letting him win at pool to keep him in a good mood, threatening to punish Francis if he loses again, while the other cadets threaten to beat him up if he wins. When Francis misses an easy shot, Spangler starts trying to throw the match, resulting in both trying their best to lose.