Malcolm accidentally hits a ball into grouchy old Mrs. Griffen's yard and, when going to retrieve it, he has a run-in with the old lady, accidentally making her fall and break her arm. As punishment, Malcolm must go over to Mrs. Griffen's house every day after school to help her out; Dewey begins carrying a purse to school rather than a back pack; Francis must deal with his screw-up friend Richie at military school.
Lois and Hal try to end Dewey's dependence on his stuffed animal Domingo by convincing him that it is too dirty. Strangely attracted, Malcolm finds himself in emotional confusion about the new weird Krelboyne girl Cynthia. At the academy Commandant Spangler re-institutes old Hickory into the school's disciplinary system and Francis tries to convince his father Hal to lie for him to avoid punishment.
A new family moves into the next house and the family tries to make friends with them. As it turns out, all but the two men despise each other, which leaves them living their new-found friendship in secrecy. Francis finds Commandant Spangler emotionally devastated, questioning his own accomplishments, comparing himself to a prominent visitor to the academy.
Hal feels like his job is a piece of crap after going to Dewey's class for parent job day. So he decides to take a "kidney failure" weeks off. While Francis is forced to work at the lucky aid over spring break.
Lois' estranged parents, Ida and Victor, pay the family a visit. Right away, trouble starts brewing. Victor bonds with Reese, Ida gets Malcolm into a fight, and Dewey is haunted by childhood memories of his inattentive grandparents. To make matters worse, Grandpa Victor gives Reese a live grenade as a present, and worse comes to worse, the boob pulls the pin! Luckily the family survived the explosion, but their brand new, expensive refrigerator wasn't as lucky.
Francis organizes a hunger strike to get back the academy's TV, taken away by Commandant Spangler. Meanwhile Malcolm has to go to the hospital, leaving him in the children's ward and the family without their genius middle son.
In an attempt to change the usual punishment pattern for Reese, Hal signs them both up for cooking classes, which turns out to be Reese's area of genius. Meanwhile Francis gets Eric into trouble because he did not yet finish his part of their co-op history assignment. Malcolm has the best intentions when he tries to explain to Cynthia that her planned party might end up with less then expected attendance.
Francis is home to repair the roof, while Reese has even more troubles with his grades then usual, although he is convinced that his Teacher Mr. Woodward is out to get him. While Dewey makes a new friend, Lois makes Malcolm tutor Reese and Malcolm soon finds out that Reese was right about Mr. Woodward all along.
In this special episode, we see what would happen if Lois took the kids bowling and what would happen if Hal took them bowling. Lois keeps the kids under tight watch, making Malcolm's night miserable, since he's the worst bowler in the group; Hal is on the verge of a perfect game, Reese ticks off the wrong guy and runs for his life, and Malcolm finds a girl who is attracted to him.
In this episode Craig still lives in Lois and Hal's house, because his one had been burnt down. That costs a lot of things on the whole family. Meanwhile, Malcolm and his brothers find a mini-bike in the garbage. At first they argue with each other, but after their mother banned the use of the bike, they join forces against her. At the same time Hal goes to Allabama to visit his son Francis for the Fathers-and-Sons meeting, where he expects some great achievements from his son. But what will happen after all that ?
When the family gets a new couch, Hal loses the old one on the way to the dump, causing a train accident with dire consequences for the whole neighborhood. While Hal tries to make it up to society, Dewey makes people believe he is an orphan. Reese starts a black market, while Malcolm is grounded and confined to the bunk in the emergency camp. Meanwhile Eric takes Francis on a somewhat different double-date.
Lois is two weeks late with her period, causing her and Hal to panic and start a big fight, while trying to keep it from the boys. And while Dewey is scared that his parents may split up, Hal and Lois remember the troubles of getting their previous four sons.
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, arriving in Alaska to begin working with his former classmate, Eric, Francis learns quickly that his great expectations are more like a wilderness nightmare, and his new boss, Lavernia, may be the icing on the tundra.
Dewey tries to prove 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.