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.

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.

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.

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.

Trouble finds Reese at his new fast-food job; a new Krelboyne tutors Malcolm; Hal and Lois sabotage Dewey's plan to get a dog.

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.

With the arrival of their fifth child, Lois and Hal search for a "creative" daycare solution.

No one wants to tell Stevie his parents are getting a divorce, until Reese spills the beans.

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.

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 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 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.

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.

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.