Reese tries to escape his army duty after landing in Afghanistan, even as Lois tries to come to his rescue. Malcolm tries to keep up the mischief of Reese by acting up in his absence.
Dewey's departure from the special needs class leads other to follow and take up residence in one of the family's trees. Hal takes charge of a bodybuilding group.
Hal gets into a garbage brawl with the garbage man when his family is called slobs. Lois and Malcolm have a work disagreement over a racially charged standee that escalates.
The girl next door plays Reese and Malcolm against each other when she convinces each that the other is gay. Hal creates a new holiday, Pearl Harbor Day, and decorates his house accordingly.
Kitty turns to Lois for aid in getting Abe back. Dewey is terrorized by a visiting Francis and his initiation into the "brotherhood." Reese discovers that he has multiple layers of skin and ruins Stevie's award acceptance speech.
Hal lies about a Christmas present that he has for the family when he becomes jealous of the gifts that Lois and the boys have.
Hal develops a sleepwalking problem as a result of stress from his upcoming anniversary. When Reese discovers that he can get his father to do what he wants while in the sleepwalking, he quickly starts to take advantage of his newfound power.
Lois turns to Francis to rekindle her motherly spirit after Jamie nearly kills her with a cabinet. Reese feels the maturity growing within him pushing against his dangerous streak, so Dewey and Malcolm arrange an extravagant send-off for it.
Malcolm's dream car turns out to be a bust. Lois seeks Hal's help in undoing a terrible hair cut which brings out Hal's natural talent in that arena.
When the boys spray paint a strip club billboard and are caught by Lois, Malcolm decides to turn the prank into a protest hoping to deflect her anger. His plan backfires when it starts a rally and media circus.
Hal feels betrayed by the king size bed Lois purchases, thinking she's seeking more space away from him. Dewey uses this drama and his newfound love of opera to compose "The Marriage Bed". Malcolm and Reese build a street luge.
Hal finds himself literally paralyzed with indecision after he's named a neighbor's will executor and must decide whether to keep them on life support. Craig turns to the boys for help in dealing with a bully that turns out to be Craig's father.
Hal builds a tiki lounge in his garage in an effort to spend more time with Lois which serves to reveal truths hidden from the other. Malcolm earns money for the Booster Club through the embarassment of its members after Herkabe blackmails him into joining.
Dewey seeks out the leg his Grandma Ida lost while saving him from a truck. Dewey attempts to secure the leg for burial. Lois asks Francis to find a commonality with Ida so he can take care of her. The commonality they find is that they both dislike Lois's bossiness. Malcolm and Reese fight to avoid having the other glue their face to the floor.
Dewey's classmate Chad wreaks havoc in the household. Malcolm and Reese learn their true positions in the social hierarchy when Malcolm shows up to school on a skip day.
Hal's motorcycle trip with Francis for Francis's 21st birthday leads to his realization that his son has become a man without him. The trip is held against the wishes of Lois and Piama. Malcolm tries to hide inside from a very large bully who is actually at the wrong house.
Malcolm makes a deal with Norm, a man living in Lucky Aide, that he won't rat him out if Norm provides Malcolm details on a crush. Reese tries to set himself up as a exterminator by releasing caterpillars on the neighborhood. He decides he can't kill them and ends up with butterflies.
Malcolm gets an F on his first music appreciation assignment and asks Dewey for help in that area. Lois, afraid that her mother is going crazy, visits her at a community center where she's actually making friends.
Dewey takes up with another neighborhood mother even as Reese bonds with a dog pack. Hal is appointed the motivational leader for the company when the scheduled leader disappears.
Hal accidentally winds up with an $800 phone sex charge after he calls to complain and then forgets to hang up. Malcolm replaces the Uncle Sam on stilts outside Lucky Aide, earning his wrath. Reese tries to make money volunteering to test experimental drugs. Dewey tries to learn of the secret stash Jamie keeps producing jewelry from.
Hal and Malcolm have differing agendas after Hal runs for President of the Neighborhood Association. Dewey helps Francis at his new camp activities coordinator job. Dewey's classmates make hostages of the school's principal, their teacher and the janitor.
The boys enter their mother into the Mrs. Tri-County Pageant on a lark, but come to her aid when they hear her being jeered by other contestants. Mr. Herkabe has Malcolm acting as a go-between for him and a contestant.