Bart, fed up with Homer's neglect, joins the Big Brother program posing as an abandoned child so he can hang out with a better father figure. Homer finds out about Bart's cool, new friend, Tom, and exacts his revenge by donating his time as a big brother to a real orphan named Pepi.
After playing soccer, Bart waits for Homer to pick him up. At the Simpson residence, Marge reminds Homer to go and get Bart on her way out the door—Homer says "I'm on my way", but unknown to Marge he is saying this because he is watching Wheel of Fortune and the exposed letters spell out "I'M ON MY WA*". Homer was so focused on the game show that he didn't hear what Marge said, and he forgets to pick up Bart. Bart is left alone as a storm approaches. Many occurrences at home remind Homer that he was meant to do something, but he cannot recall what. When Homer finally remembers after a dream about seeing Bart's skeleton on a soccer field, he rushes out to pick up Bart (who is very angry) and tries to put the issue behind them. But Bart is not buying.
When they return home, Bart watches TV when a television commercial for a mentor program called Bigger Brothers comes up. This gives him an idea and he goes to the Bigger Brothers Agency disguising himself with accent as a brave young boy whose father left him six years ago. Afterwards, Bart is assigned a big brother called Tom whom Bart first meets when he comes to school to pick Bart up by letting him ride on the back of his motorcycle. Later on, Bart and Tom meet up for Tomato Day at the Springfield Stadium (the purpose of the tomatoes is revealed when a recruiter for the Springfield Communist Party is introduced on the field before the start of the game; he is pelted with tomatoes before he can begin his speech, and remarks that it is at least better than "Dart Day"). Afterwards, they go to lift weights and watch Ren and Stimpy. Eventually, Homer finds out about Bart's Bigger Brother and angrily confronts him about the issue. Homer decides to go to the Bigger Brothers Agency to get revenge by being assigned a replacement son. There, he is assigned the child Pepe (whom he calls Pepsi for a brief period). Homer shows Pepe the garage door, "a wonder of modern technology" and then the two look at the stars together.
Meanwhile back at the Simpsons household, Marge finds a $378.53 phone bill for calls made to The Corey Hotline. Because of this, Marge headed up to talk to Lisa who is hiding in her room, as the entrance is decorated with a Corey poster. Marge tells Lisa that she understands what Lisa is going through and that when she was a girl she had a crush on Bobby Sherman. This revelation causes Lisa to laugh uproariously. Even so, in the end Lisa promises her mother "...you'll never be billed for another call." However, Lisa continues to make calls to the hotline from such places as Doctor Hibbert's office and from a phone at Springfield Elementary. After Principal Skinner catches her calling the hotline, he calls Marge. In Skinner's office, Marge suggests that Lisa try to go until 12 o'clock that evening without calling the hotline; if she can do so, she will have conquered her addiction. Lisa is eventually able to make it after a struggle.
Elsewhere, Homer takes Pepe to Marine World to attend Big Brothers Day. Tom also takes Bart there. After Homer runs into Bart, Tom tells Bart not to talk to strangers and begins to lead him away from Homer. Homer states that he is Bart's father. As Bart has told Tom many false stories of Homer being a terrible parent, Tom halts and asks Homer with barely-restrained anger "His father, the drunken gambler?" Homer instinctively and cheerfully replies "That's right, and who might you be?" Tom punches Homer in the face, beginning a brawl between the two men that rages across Springfield. In the end, Tom punches Homer which causes him to bend painfully backwards over a hydrant. Homer ends up in a stretcher and Bart—who feels guilty for indirectly causing the fight—gets ready to ride with him to the hospital. Tom is left without a child to take care of and Pepe without a Big Brother. Seeing this, Bart makes an obvious conclusion, telling them that Tom should become Pepe's big brother. Tom and Pepe agree and start hanging out with each other. Afterwards, Bart and Homer reconcile and the episode ends with them sitting on the couch, Homer teaching Bart how to fight dirty (like he did with Tom).
According to DVD commentary, the entire part where Krusty is on Tuesday Night Live was Jon Vitti's way of criticizing Saturday Night Live at the time of the episode, which was being criticized for having overlong sketches with thin joke premises (and criticisms of this kind for SNL continue to this day), which explains Krusty's line about The Big Ear Family sketch going on for twelve more minutes, even though the joke's punchline was well established. The sequence originally had a longer version of the Tuesday Night Live band playing into the commercial break, but cut it because he didn't want to come off as being bitter (Vitti, along with writing this episode of The Simpsons, was a writer on Saturday Night Live during the 1985-1986 season along with fellow Simpson writers, George Meyer and John Swartzwelder).
Also mentioned in the commentary is that the role of Tom was written with Tom Cruise in mind. However, after being repeatedly turned down by Cruise, the producers went with Phil Hartman. This is probably why Tom is an F-14 pilot, according to Bart.