Malcolm gets a job working for Lois on the drugstore loading dock but is shocked to find that Lois smokes. She makes him promise not to tell, then turns her back on him and writes him up for a silly offense. Meanwhile, Dewey runs away to the Ranch to be with Francis because he says he is tired of Reese and Malcolm. Hal is also busy, secretly betting on and entering Jaime in baby competitions.
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.