Malcolm gets his tongue pierced and needs to hide it for a month. While Lois' mother, Ida, comes and annouces that she will marry a rich Chinese Man that she met on a cruise. Malcolm gets complications when his tongue ring gets infected, rendering him unable to say "S's" and he discovers that Ida has been drugging her fiancé with opiates and mood enhancers. When Lois and Hal confront Ida, she drugs them with free food. But luckily, the fiancé misses a drug treatment, and realizes that Ida is a terrible woman and he leaves her at the altar. Malcolm is punished for his tongue piercing. Meanwhile at the ranch, Otto decides to hire a murder mystery acting troup, but it all turns out badly.

Lois tags along with Malcolm as he visits a college, but she's determined to room in the dorm Malcolm is staying in when she learns the room is co-ed. Meanwhile, after his father denies him a piano, Dewey begins stealing objects from around the house to amuse himself and to drive Hal crazy. Reese meets a girl, who he thinks is a narc, and he pretends he is a dealer, unaware that she is really an undercover cop.

Reese continues to be a great soldier in the Army until he finds himself in a situation where his Sergeant cannot help. But after comparing being captured to being grounded, he takes action and leads his team to victory. But being such a successful soldier has it's bad parts as well, as Reese prepares to jump from the plane - right into Afghanistan. Malcolm has his hands full as well as he attempts to prove Hal innocent. But being good with numbers helps as Malcolm notices all of the prosecutions given dates are on Fridays - which Hal hasn't worked on in over 15 years. And with Reese missing and Hal's case, Lois falls deeper and deeper into insanity.

Malcolm and Reese plot revenge after they realize their teenage neighbor has tricked each of them into believing the other is gay. Meanwhile, Hal, tired of competing with a neighbor who always outdoes his Christmas decorations, decides to create his own "holiday" to decorate his house for - Pearl Harbor Day.

Kitty returns and asks Lois for help getting Kitty's estranged husband back; Francis comes home and puts Dewey through the torturous "Brotherhood Initiation."

When Malcolm spots a roughed up 1967 Cuda in his neighborhood, he instantly falls in love with it and purchases the car. But he gets so caught up in the difficult task of restoring it that he blows off Stevie as well as Reese who needs him for an illegal betting scheme of his. Hal on the other hand, is having success when he stumbles upon his hidden talent -- hairstyling. Lois doesn't have time to worry about Malcolm or Hal, as she is caught up in scandal between Craig and their Lucky Aide boss Fred. Craig says he is taking time off to tutor Fred's wife in golf but Lois finds out he is actually having an affair with her.

When Hal and Lois realize how little time they spend together, Hal turns the garage into a private tiki lounge where he and Lois can retreat. Things go smoothly until they feud over philosophical beliefs. Meanwhile, Mr. Herkabe cons Malcolm into joining the Booster Club, where he learns a lesson about taking one for the team.

The family attends the counterculture Burning Man festival in the desert.

When Malcolm gets paired with a dimwitted beauty as his chemistry partner, he thinks it's a recipe for disaster, but when she reveals her feelings for him, sparks fly. They agree to keep their romantic experiment under wraps until Malcolm realizes that she's just embarrassed to be dating him. Meanwhile, Lois demands that Reese get a job, and she kicks him out of the house to prove that she means business.

When Lois finds renewed energy with orthotic inserts for her shoes, Hal fears she will not look to him for support anymore and plots to destroy the inserts. A former female army buddy of Reese's comes to their house for a visit. But she gets defensive when Reese thinks they are way more than just friends and comes intact to the idea of trying to sleep with her.

A broke Francis gets talked into getting a real job by Dewey, but one of Francis' rocker friends decides to offer him the position of tour manager of his band instead. Back home, Hal takes over the college recruiters, which Malcolm refuses to meet with, and treats each one as a suitor. However, Hal's plans are ruined when Malcolm chooses to go Harvard.

Reese meets a cute vegetarian named Carrie when he goes back to work at the meat plant. At first, he goes along with her political talk, but she catches him with a pork chop. So, to get Carrie back, he sets free all the cows at the meat plant. Malcolm, meanwhile, tries to fool Lois in order to attend a rock concert.