Hal has a dream that leads him to Vegas in search of his fortune, a giant slot machine. Also, Reese and Dewey enter their giant rabbit in a contest in Sin City and Malcolm tries to make up his insulting Lois by taking her to a concert.
A night of babysitting for an exhausted Lois spins in ways no one could have predicted. First, Hal gets stuck at Lucky Aid when he's accused of shoplifting by Craig. While Reese and Malcolm abandone Dewey (who babysits Jamie) for a couple of girls.
Abe refuses to tell Stevie that his mother isn't coming home as he had promised. So Reese takes it upon himself to deliver the news. Also, Reese finds the diary of what he thinks is his dream girl.
Meanwhile, Francis and Otto must contend with their duties as "real" ranchers when a horse needs to be put down.
Reese finds that making Thanksgiving dinner is harder than he thought, and Malcolm ditches the dinner to go to a party.
Malcolm's teacher, Mr. Herkabe, tricks him into filming Reese on his most tender moments, and then humiliates Reese and makes Malcolm seem like a monster.
Malcolm gets a job at the super market where Lois works, Hal enters Jamie in a baby competition, and Dewey runs away to the ranch to live with Francis.
Hal and the boys sell Christmas trees, but must outsell the church to make a profit. Francis celebrates Christmas with Otto and his family, and watches while they argue.
When the Wilkersons came back from their vacation they found out that the whole block was making a huge party to celebrate that they were gone. While Lois and Hal join a sausages-eating contest, Reese and Dewey start to make money by torturing younger boys and Malcolm, without knowing it, helps a thief to steal everything in the garage of an innocent family.
Malcolm tells the A.C.L.U (a group that's against the unfair censorship) that they are censoring the almost inoffensive school magazine which is just defending people's rights. Meanwhile, in order to get his old salary back, Hal attempts to flirt with the woman who's responsible of the salary cutbacks.
Jamie's babysitter asks Malcolm to do a small job for her. He accepts without knowing that this "task" involves messing up with Jamie's babysitter ex-boyfriend and a huge family problem. Meanwhile, Dewey's new friend leaves him and befriends Reese while Francis encourages Otto to face an old enemy who almost stole Gretchen from him.
Malcolm gets a tongue piercing. In a month, he'll be able to take off the piercing while he's at home; however, he has to wait that long. Unfortunately, he notices that he can't pronounce letter "S", making obvious that something is happening. Furthermore, his tongue becomes infected. Meanwhile, Ida announces that she'll marry a rich Chinese man that she met on a cruise, but Lois and Hal find out that she's drugging him.
Lois makes Malcolm play softball, but he ends up doing a terrible job because Lois doesn't let him play well. Meanwhile, Hal accidentally became a CIA's agent, Reese tries to beat a very stupid record and Francis becomes an annoyance for Lois.
Lois younger sister, Susan, visits the Wilkersons and gives expensive and cool presents to the boys while she ignores Lois and Hal. Lois and Susan have been enemies since they were very young girls. Their relationship becomes especially bad when Susan gives Malcolm and Reese a luxurious Mustang. However, when Lois finds out that her sister is very sick, her thoughts about Susan change and now she feels that she should help her.
Lois gets incredibly angry because they charged 15% more to their bill at their favorite pizza restaurant. Meanwhile, Malcolm started to date a girl, Angela. She tells him that her family is strange and usually hates her boyfriends; however Malcolm's intelligence fascinates them. He ends up going to see Angela's family, but he forgets about her in the end....
Reese rents an apartment after being thrown out of the Wilkersons' house - but finds it difficult to avoid debt. Malcolm helps a football player write an essay to get him into college. However, when the sportsman turns out to be even stupider than he thought, he is faced with a dilemma.
Lois accompanies Malcolm on a visit to his new college - and insists on seeing his dormitory. Dewey starts stealing items from around the house to get his own back on Hal, and Reese has an unfortunate encounter with an undercover police officer.
Hal plans a blind date between Polly, Jamie's babysitter, and Abe. The date is very successful, but he finds out that Lois also planned a blind date between Polly and Craig!
Dewey is about to make an I.Q. test that will determine if he'll be in the normal class, the Krelboyne class for smart children or the "special" class. Since Malcolm knows that Krelboyne's are always annoyed by their normal classmates, he convinces Dewey to get horrible results. However, the results are really awful and he is sent to the special class for Emotionally Disturbed Kids.
When Lois and Hal force a reluctant Dewey into the humiliation of door-to-door candy bar selling, Dewey adopts underhand tactics to get through the unbearable task. He tells each one of his neighbors all profits will go to good causes - and sales go through the roof.
Meanwhile, Malcolm and Stevie are wracking their brains on an impossible science experiment.
Lois discovers that her dad had another family. She goes to visit his "other wife" and learns some shocking secrets about her dad.
Hal is falsely accused of a crime involving his company. Lois goes crazy, and Reese runs away when he sees Malcolm with his girlfriend. Francis and Piama must take care of the house and Lois.
Reese continues to serve in the army, Lois is still insane, and Malcolm is trying to prove Hal innocent. When Malcolm finds out a shocking secret that can prove Hal innocent, everything could be fixed.