There's a new girl in the Krelboyne class. Malcolm learns that his dull pencils were part of an elaborate yet unknown hazing. Cynthia is a fresh recruit from New York, and she earns Malcolm's affections with wit and Israeli ass whoopin' moves. But she's wweird; she picks earwax while flirting. Of course, Malcolm throws bricks through windows, so they're a match. Meanwhile Dewey is wearing a home made hazmat suit hugging all the home's scary germs, because he doesn't want to lose his eyes. And, Francis, he hasn't done anything worse than usual, but Hal lies for him. Hal feels guilty. Francis must pay. One hopes this means Francis will get over his mother, his future therapist has to catch some kind of break.
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.