Malcolm beats up an annoying 7 year old named Kevin. Hal cuts down a tree in their yard, and the neighbors become angry. Malcolm, Reese and Dewey hold a funeral for their frog and send him up to space on a firework. Meanwhile, Francis tries to get out of a disgusting sex education talk by stealing slides of it and replacing with Commandant Spangler getting in trouble with the law back in his youth. However, he underestimates Spangler when he shows a cunning and trickier side by replacing his slides of youth with those of Francis picking his nose and urinating drunk. At Malcolm's school, Hal angers the neighbors more when they catch him beating up a man who turns out to be the same age as Francis.
In the cold opening, the boys are in the backyard hosting a funeral for their deceased pet frog Jumpy #9. Malcolm delivers a respectful eulogy as Reese remembers sticking Jumpy in their mother's sun visor and how hysterical it was she almost hit a lady in a crosswalk after being surprised by him. Malcolm bids farewell to Jumpy #9 as they attach him to a firework as Hal lights it for them. After being shot into the sky Reese says "may he rest in pieces".
The episode opens with Malcolm and Stevie playing catch in the school ground, until their baseball is lost and found by Kevin, a bullying, obnoxious new kid who has only been at the school for two weeks and has already earned the disdain of all his fellow students. He begins imitating and mocking Malcolm, until Malcolm recites a complex chemical name and Kevin is unable to copy it. He then says, "You stink, your new name is Stinky! If you want your ball back, go get it!" as he throws Malcolm's ball across the schoolyard.
Back at the house, Hal and Lois carry an injured Dewey inside after he attempted climbing the tree in the front yard. Hal decides he's had enough of the tree causing problems and says it's high time it was cut down. Dewey asks if he can help kill it, Hal agrees claiming they can take turns.
Meanwhile, Francis vies with his intimidating military-school commandant Edwin Spangler, a brutal, one-eyed, 4-fingered, hook-handed, brace-legged disciplinarian who's presenting fear-mongering sex education lectures.
When Malcolm is waiting in the lunch line, Kevin cuts in front of him and claims the last of the frozen pizza, leaving him with American goulash. After sitting down, Stevie ponders the unappetizing-looking food, and Malcolm can only identify a carrot and what he can assumes are Skittles. Kevin then comes over and brags about his pizza that Malcolm didn't get, taunting him and further verbally assaulting both Malcolm and Stevie. Malcolm warns Kevin to leave him alone, but Kevin only becomes more obnoxious, chewing pizza messily in front of him. Malcolm has had enough and pounces on Kevin, pounding him senseless with all the other kids, and even Rowena the lunch lady cheering him on. Unfortunately his victory is short lived. After Kevin is taken to the nurse's office, Malcolm learns that Kevin was only seven. Malcolm is in disbelief, as Kevin is bigger than him. Malcolm's Krelboyne teacher, Caroline, comes in and is in shock, blaming herself. Malcolm is guilt-stricken, stating it to be the worst thing he's ever done. He attempts to apologize to Kevin, but the nurse tells him he's done enough, with Kevin saying it was the worst birthday ever (meaning he just turned seven and was six previously). The nurse shuts the curtain, preventing Malcolm from soothing his guilt about the situation.
Walking home, Reese is reading Malcolm's form and is impressed as he has been called a thug, claiming it to be the equivalent of an Oscar. Dewey asks Malcolm if he can beat up a girl named Susie Gunther who ate his crayons. The three boys then notice their father had cut down the tree. Hal explains it was a once in a lifetime event when soon after the trees foundation gave way a large amount of squirrels ran out of the tree and were chased away by a pack of dogs that came out of nowhere. Reese and Dewey are disappointed they missed out but Hal tells them that they'll get to share in the best part: cleaning up.
At breakfast the next morning, the family benefits from the tree being gone, adding light into the kitchen and eating robin eggs. Hal states there must be a lesson that the tree took 100 years to grow and only 12 minutes to come down. Malcolm then asks when his parents will punish him for beating up Kevin, all of them burst into laughter. Both parents believe that Malcolm was in the right, and Hal informs him that since Kevin didn't listen to Malcolm's warning, he was merely asking to be beaten, calling it an honest beating mistake. Reese thinks it sends a good message to their enemies, Malcolm only noticing that his family members are all crazy. Lois answers the door to Ed and other neighbors who are angry at them for chopping down the tree, claiming removing trees is a neighborhood decision. Lois only adds that the neighbors have mowed their lawns at night so they don't have to talk to them. Ed refutes that removing the tree is a blight because now they can all see their house. Lois and Hal furiously tell them off with Reese and Dewey joining in, but in Malcolm's mind, they all holler like gorillas, before accidentally scratching under his arm like an ape.
Malcolm then visits a priest at a Catholic Church, a rabbi at a Synagogue and a new age guru to help him with his guilt. All three lecture him about salvation and sin to the beat of a catchy song and mashed-up montage, telling him it's mostly common sense and he'll be fine if he 'aligns his spine'.
Reese and Dewey come up to Hal, who has a wood-chipper to help clear the debris. Hal asks where Malcolm is, and Reese claims he said something about being evil and ran off. The boys are fascinated with the wood-chipper and the three of them throw things in such as a lunchbox, a Hawaiian shirt, a watermelon, a basketball, a teddy bear, and a box of confetti. After the confetti, Hal states they must be out of ideas.
In class the next day, Malcolm talks to Stevie about his problem whilst Eraserhead directs a play. Stevie couldn't care less about his problem, claiming it'll blow over. Malcolm then finds a flyer for a charity marathon race and decides to enter it, knowing once he finishes, he'll know he helped raise money to help cure diseases, then and only then he can move on.
Francis tries to prank his authorities by convincing Stanley to sneak into Spangler's office and switch the slides for the sex ed presentation. However, the Commandant hijacks their plan before it comes to fruition and puts some very different slides in instead in the form of embarrassing photos of Francis picking his nose and the like. Afterwards, he tells Francis that a general always "checks his chamber".
Malcolm trains for the race by being chased by a large dog and gets monetary pledges by using Stevie's wheelchair to manipulate people's sympathies. Hal and Reese plant a new tree but realize how different it is from the old one and miss it, with Hal telling Reese to go get his chainsaw. Hal is then approached by a large man who confronts him about Malcolm beating up Kevin, and is implied to be a relative of his.
At the race, Hal explains to Lois that he beat up the man, unaware he was a teenager only 15 years old, but claims how huge he was and how strong of a grip he had on his throat. Caroline is pleased with Malcolm for signing up, and having more pledges than any of the other runners. Hal asks Lois if there would be any beer being sold but Lois reminds them they're at a charity event at an elementary school. Caroline approaches Malcolm's parents informing them if he runs the distance, he'll raise over 8,000 dollars. Once the starter's pistol fires, Malcolm takes his first step and trips, rendering him incapable of completing the race.
In the bathroom Lois is applying rubbing alcohol to Malcolm's knee, and wonders why he's been behaving differently. He tells his mother that he can't stop feeling bad for beating Kevin up and he feels like he has a monster inside him. Lois tells him point blank that it isn't a monster, it's his conscience and he should be thankful that God gave him one. She then tells him he'll only feel bad about Kevin as long as he's supposed to but then it'll fade over time and become a forgotten memory. She tells Malcolm he's a nice boy and she will personally kick the conniption out of anyone who says otherwise, including his conscience. They then bid each other good night, with Malcolm already starting to feel better.
- This episode marks the first appearance of Commandant Spangler.
- This is also the first time Eraserhead has a major role in the episode that isn't just a background cameo.
- School scenes were shot on a specifically built set on the most northerly point of the CBS Studio Center.
- Malcolm is chased by a dog here.
- During the montage of Hal and the boys throwing things into the wood chipper, one of the things that was thrown in there was a Winnie the Pooh doll.
- The tree that Hal cut down appears again, perfectly intact in all subsequent episodes. It's impossible this was the replacement tree.
- The Latin phrase that Malcolm uses to confuse Kevin is "de gustibus non est disputandum" meaning "In matters of taste, there can be no disputes" (literally "about tastes, it should not be disputed/discussed").
- At the race Hal tells Lois he wants to get a beer. When she reminds him that he is at an elementary school outing he mentions having to go to a stand. This is a possible reference to the California Highway Patrol's request to the state's professional sports teams to not have beer salesmen walking up and down the aisles (forcing those wanting a drink to seek out a stand) in an effort to curb drunk driving, a request most teams have abided by.