The family takes a vacation with the Kenarbans, sharing a houseboat. And while Steve's parents are caught in a fight, Reese and Steve socialize with some cheerleader from a nearby spirit camp, Malcolm is stuck with Hal fishing. At the military academy, Eric turns eighteen and leaves for Alaska, inspiring Francis to do something about his situation too.
Lois, in an attempt to get a break from the family, joins a book club that turns out to be a night off for frustrated housewives, but it all goes a little bit haywire. Meanwhile Francis tries to get to Alaska, learning something important about himself and about truck drivers. Hal, who tries to keep the boys out of troubles for the evening, is caught in an inner conflict about how to treat them.
Francis has to stay a couple of days in a small county jail and enjoys it more then he expected. Malcolm finds himself with a girlfriend, which add to his usual social anxiety. Dewey makes friend with a new kid in the area, helping the kid's mother to compose Dewey's dream birthday party for his new friend.
Malcolm, Reese and Dewey "volunteer" to do charity work at the local church. They soon begin bartering the many items in the church basement in exchange for money, but when the boys start making more of a profit than the church, their consciences finally catch up to them. Meanwhile, en route to Alaska, Francis is utterly humiliated by a boisterous truck driver.
Dewey tries to proof he can take responsibility by taking care of the class hamster for the weekend, his efforts being ignored by his parents who secretly try to wait out possible bad news from Hal's doctor. Meanwhile Reese and Malcolm try ditch home for a party and Francis has to fight Lavernia, his boss.
It's another Wilkerson family Christmas- Reese, Dewey and Malcolm misbehave a time too many, so Lois moves the tree and all the presents to the garage, which she called, "holding Christmas hostage". While Francis, much to his chagrin, goes to Canada to visit Grandma Ida, whose Christmas spirit was running on empty. Much like her gin bottles.
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 Kerlboynes are forced to re-join the rest of the school, to disastrous results. Dewey is stuck and home with chicken pox's and builds a dominoes masterpiece, that Hal wants to knock down.