The Wilkerson boys plan to sneak off to a New Age festival in the hope of seeing some naked women, but when their parents find out, the trip becomes a family affair. Malcolm falls for an older woman, while Lois goes topless after discovering the joys of hemp.
Hal forgets to pay the family’s health insurance and when the company won’t reinstate them until Monday, he panics and locks the boys in their room so they won’t get hurt. But the boys try to escape, Jamie gets in harm’s way and Hal is the one who needs a doctor. Meanwhile, Lois and her coworkers discuss unionizing at the Lucky Aide and she hits her 10-year anniversary at the store.
When Hal catches Dewey smoking, he makes a pact with him that he'll stop drinking coffee if Dewey kicks the habit, but after a few unsuccessful attempts to beat their addictions, they both start sneaking around. Meanwhile, Reese picks a fight with Stevie and their confrontation gets heated
Malcolm and Reese go on a tour of the neighborhood for Halloween, but get scared when their own house is the first stop on the tour.
The neighbor's daughter, Jessica, stays with Malcolm and the family for a week. She soon shows Malcolm how to manipulate Lois to get what he wants. Also, Reese gets into a fued with his foreign penpal and Hal tries to avoid a confrontation with a...bee!
When Malcolm gets paired with a dimwitted beauty as his chemistry partner he thinks it’s going to be a bad combination, but then she reveals her feelings for him and sparks fly. They agree to keep their romantic experiment under wraps until Malcolm finds that she is embarrassed to be dating him. Meanwhile, Lois demands that Reese get a job and kicks him out of the house to prove it.
Francis decides to surprise the family by coming home, but he catches Jamie off-guard and ends up knocking the lights out in the house. Meanwhile, it’s Lois who’s in the dark when Hal decides to cancel their anniversary dinner and forces Reese to cook them a romantic feast at home, and Malcolm who ends up in hot water when he sneaks three Swedish girls into the house.
Hal enjoys pampering an aching and exhausted Lois, but all that changes when she buys orthotic inserts for her shoes and has renewed energy – so Hal plots to destroy the orthotics and get his weary wife back. Meanwhile, Reese’s Army pal pays a visit, but she gets defensive when Reese thinks they’re more than friends.
Lois finds a new babysitter for Jamie who is wonderful until she opens her mouth and starts to drive Lois crazy. Meanwhile, Malcolm and Reese are in the same class, but Reese is the one being picked on by the teacher – until Malcolm stands up for him.
Malcolm gets a check for his college fund but never sees it as Hal and Lois intercept. A debate soon erupts over what they should do with it (new water pipes or a boat) until someone else wants in. Meanwhile, Reese gets into (and causes) trouble when he starts hanging out at the nursing home.
When Lois and Hal take Dewey out of town for a piano competition, they enlist Grandma Ida to watch over the boys. Ida thinks that Reese needs to become a man, so she forces the two brothers into a competition and if Reese wins he takes Raduca as his bride.
Meanwhile, when Lois and Hal return home they're shocked to find out Reese has run off to Vegas.
Dewey visits a broke and disheveled Francis and just as he talks him into getting a real job, his rocker friend shows up and gives him a cool gig as tour manager of the band. Meanwhile, Malcolm refuses to meet with college recruiters, so Hal takes over and treats each one as a suitor – until Malcolm chooses Harvard, which ruins everything for Hal.
Lois finds out that she has Mono when she goes to the doctor's office, and ends up giving it to Malcolm. Malcolm and Lois have to spend a whole day in the same room together, and end up bonding.
Hal gets a devastating phone call that his father has passed away, but since Hal never met his father, he doesn't feel sad. In an attempt to overcompensate with his kids, Hal takes the boys shopping, lets them miss school. Hal even offers to buy Malcolm a new car until Lois steps in. Hal's buddy Abe thinks that a visit from George Takei will cheer him up.
Lois and Hal visit Francis to help him celebrate one year of sobriety, but when they attend his A.A. meeting they find out that Lois was the one who drove him to drink. Meanwhile, Dewey finds the spare key to Hal's car, but when Malcolm and Reese refuse to drive him to the arcade, it takes them more than 12 steps to find it.
Lois decides to get revenge on four popular high school girls who play a mean prank on Reese. As she plans her revenge, Hal builds his own pitching machine in the garage.
When Hal looses his tooth during a poker game, his buddy Trey tells him to come to his dental office, but Hal really feels the pain when he's hit with a $2,000 bill that causes a rift between the two friends. Meanwhile, Reese teaches Lois how to ride a bike and Malcolm and Dewey find their new favorite pastime of sleeping.
Malcolm joins a dancing class to impress a girl, but starts to regret it when Dick, a rival student, challenges him to a dance-off. Meanwhile, Hal discovers an underground bachelor pad.
Stevie goes to the hospital, while Malcolm makes up every excuse in the book because he can't face the truth about his best friend's illness. Meanwhile, Hal gets competitive with his remote control boat and Lois thinks she's losing her mind.
Reese heads back to work at the meat plant and meets Carrie, a cute vegetarian. He pretends to go along with her politics, and he almost pulls it off until he's caught red-handed with a pork chop. To get Carrie back, Reese goes to the plant and sets all of the cows free. Meanwhile, Malcolm tries to pull the wool over Lois' eyes and sneak off to a rock concert.
Reese gets paid to take a girl named Janice to the prom, but only after she gives him a makeover. Malcolm and the unpopular kids untie and make their own party during the prom called, "Morp".
Recently elected valedictorian of his graduating class, Malcolm struggles with his speech, but Lois refuses to hear his complaints and reveals her plans for him to become President of the United States. Meanwhile, Reese will do anything to get a permanent job as the high school janitor, even concocting the most disgusting mess of all time, which explodes all over the family. At home, Hal struggles with Malcolm's Harvard tuition and Francis lands a "real" job working 9 to 5 in a cubicle and enjoys every minute of it. Grandma Ida returns for the family festivities, and they all bid farewell to Malcolm when he leaves for college.
Songs: Citizen King -- Better Days (And the Bottom Drops Out)