The house goes crazy as Hal is falsely charged in a crime involving his company which he has nothing to do with. He is put in an ankle collar and is immobile, forcing the rest of the family, including Piama and Francis, to pick up the slack.
Everyone except Reese, who is missing after he discovers Malcolm with his girlfriend Beth. The family doesn't know, but Reese has joined the Army, where he doesn't exactly understand how the military works.
Dewey also has his own problems with the family as no one listens or even knows about him leaving for a music competition.
Malcolm is a regular high school kid trying to navigate his way through life despite the various obstacles thrown in his way a complete misunderstanding of girls, the constant burden of masterminding plans to get himself and his brothers into or out of trouble, and a miserable job at the Lucky Aide not to mention a severe case of teen angst.
Although Malcolm has a genius IQ, he can't seem to make sense of the opposite sex, much less his embarrassing family. Lois is the outspoken, opinionated mom, who still manages to rule the roost even though her boys are growing wise to her crafty ways. Hal, a dad who is just a bumbling, big kid at heart, often finds himself creating more chaos than his five boys combined.