It's still summer-vacation time on the jaunty third-season opener, which finds Malcolm and his rowdy clan cruising on a lake in a houseboat with Stevie and his straitlaced parents, Abe and Kitty Kenarban. Some vacation. The vessel itself is a fright, a weathered heap that Dewey hates from the get-go because "There's no TV! There's no TV! There's no TV!" An equally distraught Malcolm is shanghaied by Hal for a fishing expedition, leaving lucky Reese the chance to trawl for bikini-clad beauties at a nearby camp. Back on board, the close quarters are slowly driving Abe off the deep end.
Still reeling over Francis' break for freedom, Lois and Hal find themselves face to face with their newly independent son. While at home, Francis wins back Hal's support, but Lois is a completely different story. Also, Malcolm and the Krelboynes meet their match when a new teacher ”a former Krelboyne himself” is assigned to the class. He sets up a ranking system that pits the students against each other and eventually drives them to the brink of insanity.
Unfulfilled Lois joins a ladies’ book club, which is really a whining—and wining—session. Meanwhile, at home, Hal’s desperate to busy the boys.
Malcolm has a new light in his life: a perky classmate named Sara (whose face, in a quirky touch, is never shown). But, according to Malcolm , she’s “good-looking and smart and cool. And if we went out together, it would make me happy. So therefore, it will never happen.” Ah, but it does—a surprising turn of events that elates the lad and perturbs his parents, especially when Malcolm goes into an academic tailspin. And it’s not long before our lovesick hero admits that he’s becoming “obsessive and neurotic, and a totally jealous creep.”
In an effort to contribute to society and to make her boys useful at the same time, Lois "volunteers" Malcolm, Reese and Dewey for charity work at a local church. The boys are assigned to sort giant piles of donated clothing, game, appliances etc. Initially irritated at their new task, they realize the donated stuff is a lot nicer than their own possessions, and they begin swapping out their old stuff with the second-hand items. The boys soon make a enterprise out of their charity assistance, going as far as to sell things to the neighborhood kids - that is until Hal finds out. Meanwhile, Francis must come to grips with the fact his fabulous job in Alaska is not quite what he expected.
When Hal's doctor discovers something suspicious during his routine check-up, Lois and Hal become frantic, nervous wrecks as they wait for the test results. As a result of her anticipation, Lois becomes even stricter with the boys, leaving them to misinterpret the new house rules. Meanwhile, in Alaska, Francis comes to blows with his boss.
When Malcolm and his brothers destroy their Christmas tree ornaments, Lois punishes them by canceling Christmas and moves all the presents into the garage. The only way she will reinstate the holiday is if the boys behave impeccably up to Christmas morning. Her plan works better than expected, and Lois is touched that her family responded so well to her challenge. Meanwhile, the boys decide that Lois could use this tactic for future holidays and retaliate by breaking into the garage and opening up all the presents. Elsewhere, Francis is forced to visit his Grandma Ida for Christmas.
Poker showdowns with Abe give Hal a flush; dance lessons turn Lois awhirl; an Alaskan blizzard entraps and rattles Francis. (TV Guide)
Trouble finds Reese at his new fast-food job; a new Krelboyne tutors Malcolm; Hal and Lois sabotage Dewey's plan to get a dog.
A negative job-performance review riles Lois; hoops play with the boys energizes Hal; a vermin infestation busies rat-killer Francis.
Juicy guest casting and ingenious plotting enliven an hourlong episode that airs in the plum post-Super Bowl slot. One storyline unfolds at Hal's company picnic, where Lois clashes with a blabby wife (Susan Sarandon) and her beleaguered spouse (Kaczmarek's real-life husband, Bradley Whitford); and Hal runs afoul of his new boss (Stephen Root) and the big cheese (Patrick Warburton). In Alaska, Francis's scheme to win a bet involves rigging a hockey game that pits loggers vs. a fearsome women's squad led by a blowhard coach (Terry Bradshaw).
After Hal is mistaken by his new boss, as that guy's boss, Hal plays along. Malcolm is in a three-legged scavenger hunt with the girl he likes, but becomes upset after he confesses he likes her, and she says she likes another boy. Reese is also the the scavenger hunt, and at first doesn't like the big dumb bully he is with, but they grow to like each other when they bond over beating up the other contestants and stealing their items. Lois continues to balance keeping Dewey intact and dealing with the crazy woman, but now must talk to the husband as well. Francis continues to sabotage his own team, this time on the ice.
Highway horror: Reese gets a learner's permit, which he promptly proceeds to abuse by commandeering a driving-school vehicle.
The return of the smart and sassy Cynthia rattles Malcolm, who's astonished by her physical maturation. And so is drooling Reese.
The arrival of Francis's new bride on Hal's birthday sparks a fray that drives the younger siblings out---and into a posh hotel.
Clever Hal invigorates Dewey's soccer team; sly Reese blackmails a philandering neighbor; obsessed Malcolm battles a computer program.
Dewey rules, thanks to his new dog that intimidates Malcolm and Reese; Hal and Lois hit the town with big plans---and flu symptoms.
Girls in the house spell trouble for the boys, who are on their own while Dad's hosting a poker game that's more about one-upmanship than cards.
An embattled psychiatrist probes the boys' naughty behavior patterns in a session framed by flashbacks to past episodes.
Lois gets jury duty and Hal tries to figure out what case she's working on. Meanwhile, Malcolm and Reese saw Stevie's mom naked and brag about it, they also take Dewey to the sewers and get lost.
Back in the general school population, the Krelboyne whiz kids wind up in cliques with jocks, skateboarders and brooding "Goths."