When Lois finds her red anniversary dress burnt and in the toilet, she immediately suspects Reese, Dewey and Malcolm of foul play, and chases them all over the house to try and make them fess up, while Hal waits all night at the restaurant alone.
While Hal and Lois are away for the weekend, Francis, visiting home from military school, is in charge of the house. Right away his friends come over and mess it up, so Francis and the boys clean it up to show Francis is responsible and might be allowed to leave military school and come home. All goes well...until a shelf falls on Malcolm, injuring him.
Malcolm finds himself being antagonized by a new bully, Kevin. This kid was always mocking him, teasing him, at lunch he cut right in front of him. On pizza day! But after Kevin taunted him about it one time too many, Malcolm loses it and attacks the kid, but deeply regrets it after learning his bully was 7-years-old; Hal cuts down the huge tree in the front yard, and he and the boys have just a little too much fun with the wood chipper.
Malcolm adores his new job of looking after the kids of a rich family, while his own family finds themselves camping out in the yard in a trailer while the house is being fumigated. Hal and Lois are constantly at each other's throats and they're all miserable, while Malcolm has the time of his life with people who seem like the perfect family. But, are they really as perfect as they appear?
Reese takes on an impossible task in order to be allowed to stay up and watch an evil puppet, while Malcolm, finding his sleepover at Stevie's a little...safe, introduces Stevie to trouble. Hal and Lois take advantage of the boys' busy evening. Meanwhile Francis, chosen as a victim by a secret cabal of tormentors, teaches them a thing or two about torture.
The family have to go to the Krelboyne class picnic. Malcolm doesn't want to go because he has to do an act and doesn't want to look bad in front of his family especially Francis who is home for the weekend. Francis promises to get Malcolm out of doing his act but meets a girl at the picnic and no longer wants to leave. Lois tries to fit in with the other parents unsuccessfully and Hal serves meat from the BBQ even though the Krelboynes all voted that there would be no meat. Reese ends up on the run from eraserheads brother who catches him in the end giving him a ...
Waiting in Lucky Aide for Lois to end her shift, Reese and Malcolm cause trouble, which leaves Dewey unobserved and able to nick something expensive from the store. Lois tries to make a point about "doing the right thing" and loses her job in the process. It also leaves the family with less income, bad food and Malcolm stressed out, especially because he already is in emotional despair over Julie Houlerman. Malcolm gets caught in an awkward social situation and Lois struggles between standing up to the man and providing for her family. Meanwhile Francis gets a break ...
Hal takes the day off and the boys to the stock car races, while Francis gets into trouble with Commandant Spangler which leads to troubles with his fellow cadets, but that can not stop Francis from aiming for the next big possibility to screw up - this time it involves a Dog and a Snake. As Lois is searching for a check, she discovers more and more dirt on each family-member, hidden in the dustiest corners of the house, which she piles up for later use. Meanwhile the boys get bored at the tracks fast and get into problems on their own.
Aunt Helen died and the family prepares for the funeral, an occasion that doesn't go as planned. Dewey finds a stray kid, Malcolm tries to avoid going altogether, Reese tries to sink some Evidence with aunt Helen's casket, Francis tries to get involved more into family matters, Hal prepares a speech, Dewey tries to get his new friend Egg home and Lois is all about family obligations. Of course it turns out much different then anybody anticipates.
While we have a chance to see the world from Dewey's very special point of view, Reese acts weird. As it turns out, he is interested in a girl and does not know how to show her how he feels. Following a misunderstood advice from Malcolm, Reese joins the cheerleader-squad. As a consequence Hal has to have "the talk" with his sons. Meanwhile in the military academy Francis gets to know Commandant Spangler on a very personal level.
Malcolm sucks at street-hockey, frankly because he has no skates. So he turns to his father, who trains all his sons in the secrets of skating before he allows them to have their own pair. Neither of his bigger brother tell him about his fathers training and Malcolm gets even more anxious as Hal gets very mysterious about it all, but nothing can prepare either one of them for what is to come. Lois hurt her back terribly and has to stay in bed, which does not keep her from tyrannizing Reese and constantly trying to avoid being drugged with pain medication by her loving...
Lois takes off to visit Francis at the academy, which might makes his recent appendectomy just a little more painful. Without Lois, Hal devolves to his former bad boy personality, which turns the Robot Malcolm builds with his Krelboyne colleagues into a much more destructive power then expected.
The boys were grounded for a while for losing Dewey's bike and can't wait for their release, but Lois is sick in bed and mistakes Monday for Sunday. But the boys appreciate the opportunity to ditch school. A letter from the academy arrives, which would cause some trouble for Francis and the boys decide to hide it, until they find out that it was Francis that sold them out about the bike. While the boys turn against Francis, Hal is at a Porsche shop and gets tempted to buy a car he can not possible afford.
The family takes a day vacation at the water-park. All except Dewey, who has to stay home with an overage babysitter, which turns out to be more fun then expected. While Malcolm and Reese get into a loop of revenge-pranks, Hal and Lois try to enjoy the day off. As Dewey's babysitter hits the dance-floor, in more then one way, the youngest member of the family sets off on his own.
As the family drives home from the water-park, they get stuck in a traffic jam. While each family members tries to deal with heat, stress and boredom in their own way, Dewey is roaming the country on his own.
Francis is a week late for Halloween, but that can not stop him from traditional festive vandalism, since he has the perfect plan to cause mischief in the neighborhood. Meanwhile Hal has to fight a different neighborhood nuisance, vigilante style.
When Lois gives the boys $10 each to buy her a present, they decide to get something for themselves, which causes her to have grief. When Hal also forgets her birthday, Lois decides that is enough, so she escapes until the family finally decides that they need her. Meanwhile, Francis brings home a beautiful African woman.
Commandant Spangler announces his mother's visit and Francis uses the opportunity to organize a dance, for which he invites some local girls, which ends up to be a very different experience then the cadets expected. Meanwhile the Kenarbans invite the whole family to a nice dinner that turns into an evening of conflicts, as the families get to know each other better.
The family is on a weekend-vacation in an native American casino. Francis uses this opportunity to go on vacation himself, by sneaking into his former home, but he is not the only one with that idea. While Hal, Reese and Malcolm get lost in the desert, Lois and Dewey enjoy a day of relaxation.
Hal and Lois heads off to a convention while the boys stays home for the babysitter. Malcolm, Reese and Dewey assumed it's just another old woman, their parents hired to watch them. They decide to do a series of pranks on their babysitter, which includes the covered up sewer tank with a blanket and a book for the old woman sit on. To their surprise, their babysitter is a hot, teen-aged girl named Patty. She is sweet to them, but also bitter because she was rejected by Francis, a long time ago, because she was obese. Now the boys compete against each other to see who ...
The night-shift at Lucky Aide is held hostage by two robbers since Craig does not want to give up the combination for the stores safe. Francis tries to help a heartbroken friend at the academy while Hal and the boys fight nature at home.
In an attempt to avoid the worst moments of medieval week at his Krelboyne class, Malcolm spins a delicate web of deception for the school therapist. Francis takes over the laundry at the academy and Hal discovers that his youngest, Dewey, is a natural at skittles.
Malcolm gets the chance to perform at a high-school play in the lead role, leaving his friends alone with their secret project. But hanging out with high-school kids and their constant exchange of useless information has quite an impact on Malcolm's mental abilities. Lois finds herself with twenty five unexpected free minutes left on her schedule, which she uses for a massage, relaxing for the first time in her life. Hal and Dewey build a giant city out of Lego, while Francis tries to fight Commandant Spangler's tyranny with flower power.
Reese, promising champion of his school's wrestling team, gets beaten by a girl, completely demoralizing him. So he gives up his school-bully carrier, which destabilizes the natural oder of things at school. Francis tries to get out of academy at his birthday in an attempt to avoid academy-birthday-traditions.