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.

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.

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 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.

Francis bails from military school in a desperate attempt to visit his stupid girlfriend.

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.

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?

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.

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.

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.

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.

When 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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

The boys and Stevie take off in the evening to visit the carnival but get into trouble, while the parents go searching for them.

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.

Malcolm gets his first official girlfriend; Dewey hijacks his new friend's birthday party to better himself.

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.

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.

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.

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.

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.

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.

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.

In a desperate attempt to get rid of his Krelboyne past and start afresh, Malcolm ends up making things even worse than they were.

Malcolm stops thinking in order to go out with a very dumb girl. Hal wins some money, and rents a steamroller.

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.

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.

Malcolm 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.

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.

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.

As Lois and Hal write their wills in preparation for the baby's birth, they recall various colorful incidents with their four current children.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

Dewey and Hal attempt to quit their vices, Reese threatens Stevie, and Lois opens up to Jamie.

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.

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.

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.

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 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.

Dewey and Hal attempt to quit their vices, Reese threatens Stevie, and Lois opens up to Jamie.

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.

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.

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.

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.

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's afraid to visit his best friend Stevie in the hospital; Reese becomes a master telemarketer; and someone secretly tries to drive Lois crazy.