In this Sliding Doors-style story, the viewer simultaneously sees what happens when the boys go bowling with Hal and what happens when they go bowling with Lois. Two subplots are also used: one where Dewey stays home with Lois and one where he stays home with Hal. In both scenarios, he is being punished for killing the neighbor's parakeet. When Hal stays home with Dewey, Dewey tricks Hal into reading him a bedtime story, which puts Hal to sleep. Now free to do whatever he wants, Dewey orders pizza and ends up watching R-rated movies on television. On the other side, he can't fool Lois, who is in control of the situation. When Dewey appears to have given up, she suspects he is up to something. Eventually, Lois allows Dewey to watch T.V., but only something he won't enjoy like C-SPAN, and neither is sure who won.
On Lois's bowling side, she warns the boys to behave themselves if they want to avoid spending one of their evenings at the laundromat. They immediately arrive at the bowling alley. However when she tries to buy two pairs of shoes, she only has enough money for one pair of shoes and forces them to share. Right away, both Malcolm and Reese notice a pretty girl named Beth (Alex McKenna) at the party, whom they assumed was responsible for getting Mr. Thomas fired. Lois soon learns that there aren't any adults chaperoning the party and demands to know where their parents are. Much to the boys' dismay, she decides to stay and chaperone it herself. Reese impresses Beth, but is constantly interrupted by Lois just before he can tell her a joke. Malcolm sucks at bowling, and is ridiculed when he gets a ball with "Connie" engraved on it. Lois's overbearing cheering isn't helping him any and only makes the ridiculing worse. When he finally stands up to her, he embarrasses himself and is further ridiculed, and Beth has had enough of Reese and her classmates. Malcolm gets a kiss from her, but Lois breaks it up and takes everyone home.
On Hal's bowling side, he and the boys get lost on their way to the bowling alley. At the bowling alley, Hal buys two pairs of shoes, having taken money from Lois' wallet, and sends the boys off for a good time, while he takes a lane to himself. Reese tries to impress Beth, but he immediately disgusts her by telling her a joke that involves spitting soda in her face and messing up her hair. Insulted, she walks away to try and recollect herself. Malcolm is great at bowling and Beth is impressed with him. A jealous Reese attempts to hit Malcolm by throwing a bowling ball at him. However, he misses and accidentally hits a large man who chases after him. Reese spends the rest of his evening hiding from the large man. Hal makes a strike and attempts a perfect game by repeating his actions (sipping his soda, putting his fly down) leading up to the strike. Malcolm leads Beth to an area behind the pinsetter machines to make out but his shirt gets caught in a pinsetter and he tumbles into Hal's lane, knocking all the pins down just as Hal is about to win. With Hal's perfect game ruined, he picks up Malcolm and orders Reese out of the auto picture booth so they can leave. The large man finally finds Reese and beats him up inside the booth (while getting pictures of himself doing it). In the end, both Hal and Lois come home with the boys saying "Next time, you take them."
"Bowling" has received positive reviews from critics, since its airing. The episode was named among The A.V. Club's "best TV episodes of the decade" for series that weren't included in their top thirty television series of the decade.The A.V. Club reviewer Todd VanDerWerff praised the episode for its "wild stylistic innovations" and compared, both the series and episode, to The Simpsons. He went on to praise Jane Kaczmarek and Bryan Cranston's performance in the episode.