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 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. ...