Malcolm is fed up with the fact that every time he complains, something wrong happens. He has recently got kicked out of the basketball team and vows not to complain anymore. He receives good results in no complaining. He recently gets back on the team, sedates Lois' anger by not taking back to her in a mean way, and the respect of his girlfriend, Nicki who shares a kiss with him. Next, Hal decides to be a speed waker and early on gets competition with a local walker. Meanwhile, Reese wants to take Alison to a concert and the only driver he gets is Craig Feldspar. ...
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.
Lois uses a long drive with Malcolm to further his sex education; Reese spends a day in prison; Dewey plants seeds of discontent in Hal's vocal group; Francis has an accident branding Otto's favorite cow.
When Hal kicks Malcolm out of the house for misbehaving, Reese tries to take advantage of Hal's distraction to come up with a truly bad stunt of his own, and Francis takes offense when Otto's musician nephew plays a musical accompaniment to Francis' every move.
The family decides to hold a garage sale to fund repairs of the bedroom wall and Lois puts Reese in charge. Hal finds his old radio-transmitter and starts running a pirate broadcast like he once operated in college.
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.
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.
The family travels to Las Vegas when Hal experiences a dream about hitting the jackpot; Dewey and Reese enter an enormously obese rabbit in a contest; Lois gets to meet her favorite singer backstage; Otto and Francis get trapped in a well.
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.
It's another family Thanksgiving, as Reese cons Hal and Dewey to help him out with the cooking. Francis and Piama are also there, but they're not even speaking to each other. Lois tries to intervene, but it goes nowhere as Hal prevents her from intervening. Soon after, all the family members start arguing with each other, claiming that this is the worst Thanksgiving ever. Meanwhile, Kirsten has invited Malcolm to her house party. He's having a blast without his family dragging him down and calls it the best Thanksgivng he's ever had in his life.
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.
Lois gets Malcolm a job at the store, exposing Lois's well-kept secret; Hal and some other fathers start betting on babies; and sick of the way his brothers treat him, Dewey travels to the farm to visit Francis.
As Christmas approaches... a layoff at work prompts Hal to make money selling Christmas trees; Francis and Piama's peaceful holiday comes to a crashing end when Otto's German relatives show up at the ranch; and Lois tries to capture a squirrel that bit Craig.