Malcolm is put in the the gifted class when a test reveals his high IQ which automatically makes him uncool. Malcolm and Stevie put their heads together to take down a bully named Spath.
Lois anticipates a lovely anniversary dinner out with Hal, but when she finds her newly purchased red dress partially burnt and thrown in the toilet, she tries to discover which of the boys is responsible. During her probing, Hal waits for her at the restaurant and drinks.
Francis takes care of the boys when Lois and Hal take a break for a wedding. In an effort to get Francis back from military school permanently, the boys band together to avoid wreaking havoc.
An annoying kid, Kevin, eventually breaks Malcolm down and Malcolm fights him. Only afterwards does Malcolm learn that he's only seven and in the second grade. Francis has a hard time deal with the commandant's sex education.
Malcolms time as a babysitter is comfortable even as his own house is being fumigated because of bugs. Francis discovers a dead body at the military school.
When Malcolm convinces Stevie to leave the protection of his home for an arcade run, his wheelchair is stolen. Francis handles the problem of bullies by regaling them with tales of Lois. Reese tries very hard to convince Lois he's old enough to stay up later and watch Child's Play.
Francis makes his way back home to visit his girlfriend and stays out of sight by hiding in the back yard.
Malcolm, upset that the Krelboyne class has to square dance in front of the rest of the school, was going to skip up until his father says taking the boys to school will be his day's highlight.
Lois's aunt dies and Malcolm has to cancel plans with Julie to attend the funeral. Malcolm tries to come up with an excuse to not go. Because of her family's reaction, Lois decides that she won't do anything else for them or around the house. Reese wants to bury evidence that he broke Dewey's birthday present.
Reese tries to land a girl by becoming a cheerleader. Dewey strives to get his parents to buy him a fancy stuffed animal named Herbie. The Commandant tries to get through to Francis by telling him all about his life.
Malcolm has to take lessons from Hal in order to get a pair of rollerskates for street hockey. Lois throws her back out yelling at Reese. Francis faces a survival weekend out in the woods and uses what Lois told him about her injury to get out of it. When Malcolm swears at Hal, Hal forces him to use all of the filthy terms he can think of.
Malcolm and his friends decide to build a battlebot. Francis has an appendectomy and decides to use it against Lois. Upon arrival, Lois stands up to Commandant Spangler which impresses him.
The boys do their best to keep Lois believing that it is Sunday and not Monday so they can avoid going to school, especially after she is weakened by illness. When they learn truthful answers for every question they ask, they learn that Francis ratted them out about what really happened to Dewey's bike. Hal is enticed by a Porsche dealer.
Dewey stays behind from a family trip to the water park because of an ear infection. Commandant Spangler learns that Francis has been throwing his pool games. Malcolm and Reese one-up each other with embarassment. Dewey breaks through to his babysitter, but after she's taken away in an ambulance, he runs away chasing a balloon.