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.

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.

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.

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.

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.

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.

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.

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.

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 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.

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.

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.

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.

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.