Abe invites Hal to his poker round for the first time. Hal is very excited until he finds out this is not as much fun as he thought ... Because Hal is busy losing his money, Reese has to accompany Lois to dance class where he becomes the center of attention of the elderly ladies. Meanwhile, Malcolm and Stevie both have creative school projects - Malcolm has to write an essay, and Stevie is making a video of this, annoying his best friend to no end.
Reese lands a part time job at Circus Burger, which seems like a good job. Until he meets his supervisor, Francis' dim-witted friend Richie, who, along with his co-worker cohorts, set Reese up as a patsy.
Malcolm and his family go to Hal's work picnic. Hal tries to avoid meeting the new boss and in return is mistaken for the boss. Dewey eats too much candy. Malcolm meets up with a girl from his past. In Alaska, Francis goes up against a girls ice hockey team in order to earn some much needed cash.
Reese and his partner from the scavenger hunt cause problems. Malcolm gets into trouble with a girl. Hal finally meets his new boss. Francis decides to cheat in the ice hockey match in order to win money. Dewey is on a sugar high.
While Dewey helps his father Hal overcoming a childhood blockade, Malcolm finds out that Krelboyne Girl Cynthia changed while away for a semester in New York and accidentally tells Reese, who comes up with a devious plan to make use of the information.
It's Hal's birthday and Lois has Francis come home to celebrate it with the family as a surprise. The surprise is on her and the rest of the family as Francis comes home with a wife he married in Alaska named Piama.
Hal has finally made a deal with Ed for the boys to have their own computer. Unfortunately, it doesn't come without favors. They find out that Ed is a philanderer and has a ton of undeleted e-mails from the women in their neighborhood to prove it. Reese sees this as an opportunity to blackmail him to his own twisted scheme. Then, Hal decides to coach Dewey's losing team into better soccer players. Meanwhile, Piama is fed up with Lavernia mistreating Francis, and decides to make her pay for it. She steals her precious parakeet and holds it hostage until Lavernia treats...
Hal has his friends over to his house for their poker game, and tries to impress them in the process. Reese convinces two girls that Stevie has a fatal illness. Malcolm discover something dangerous in the house. Dewey has no place to go.
Malcolm and the rest of the Krelboynes are forced to re-join the rest of the school with disastrous results. Dewey is stuck at home with chicken pox and builds a dominoes masterpiece, which Hal wants to knock down.
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.