Malcolm has been labeled a boy genius and is moved, much to his chagrin, into the Krelboyne class, which is a class full of nerds and geniuses like himself.

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.

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 wedgie. When Stevie leaves his chemicals with Malcolm, Malcolm desperate to do anything to get out of his act tries to make a stink bomb but ends up making a level 3 toxic bomb. The picnic seems to be ruined until Malcolm guiltily goes up on stage to preform his act. Everyone is amazed by it especially his family. Malcolm fears they will all treat him differently but to his relief nothing has changed.

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.

Lois takes off to visit Francis at the academy, which might make 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 than expected.

When Francis shows up a week late for Halloween, he and the boys still manage to create the ultimate prank; Hal tries to catch a man who keeps speeding down the street, which leads to Lois and him stealing the car.

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 will prove their eldest brother wrong in his rejection and sleep with her without sex. Meanwhile at the convention, Lois tries in vain to stop the fight between Hal and Jack, who stole his idea.

Lois finds an amazing and cheap massage table at the grocery store and manages to become so relaxed that she doesn't even care about Hal and Dewey's LEGO city.

Malcolm accidentally hits a ball into grouchy old Mrs. Griffin's yard, and when he goes to retrieve it, he has a run-in with the elderly lady that accidentally makes her fall and break her arm. As punishment, he must go over to her house every day after school to help her out. Meanwhile, Dewey begins to carry a purse to school instead of a backpack; and Francis must deal with his screw-up friend Richie at military school.

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.