The family goes to the zoo. Malcolm is going through a crisis, and he and Dewey find themselves in a unfortunate situation. Reese angers an animal at the zoo. Hal is jealous of a former flame of Lois's who works at the zoo.
Malcolm is eager to start his first year of High School and is no longer identified as a Krebloyne, but he soon discovers that his least favorite teacher Mr. Herkabe is the new vice principal and finds it hard to distance himself from his former classmates. Meanwhile Hal and Lois sign up as parental volunteers.
Malcolm and his family goes to Hals father's house for a reunion. The family doesn't like Lois. Reese and Dewey try to get in their grandfathers will. Malcolm's grandfather takes a special interest in him, while the young cousins love Francis.
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 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.