The episode starts off with an introduction by Malcolm McDowell discussing English literature. He states that Pip, the character from South Park, is based on the main character in Charles Dickens' book, Great Expectations. The self-proclaimed "British Person" narrates the story throughout the episode.
The story begins with an orphaned Pip Pirrup on his way to visit his parent's grave. While there, an escaped convict appears and threatens Pip. Pip, out of the goodness of his heart, aids the convict by giving him a sandwich and cutting the convict's handcuffs. Pip then goes home, where his sister's husband Joe reads an advertisement about a Miss Havisham seeking a boy to play with her daughter. Pip goes and meets the daughter, Estella who constantly insults him. Miss Havisham hires Pip and throughout their playtimes he eventually falls in love with Estella; she in turn is nicer to Pip and lets him kiss her.
Pip fears Estella could never marry a commoner like him. However, an offer comes for Pip from an anonymous benefactor to move to London and learn how to become a gentleman. Pip assumes the benefactor is Miss Havisham and accepts. In London, Pip meets his roommate Mr. Pocket who tells the story of Miss Havisham. He explains that Miss Havisham grew up as a rich young girl, got engaged but was left at the altar. This caused her to stop all the clocks in the house and never leave the house again. Pip spends the rest of his time in London learning how to be a gentleman, by learning "Fencing, archery, and how to eat box."
After his time in London, he shows up at Miss Havisham's house to thank her for letting him go to London, and to see if he is good enough for Estella. Miss Havisham tells Pip that he can find Estella at a party at the palace on Friday. At the ball, held by Tony Blair, the King of England, Pip and Estella dance, and talk about how Pip is now a fine young gentleman. Estella says that she has no heart, and cannot love. Right before Pip asks Estella to be his girlfriend, her boyfriend, an American seventeen year-old, Steve comes in wearing modern clothing. Estella states Steve has a car.
Pip, saddened, runs to tell Miss Havisham, only to find that she approves of Estella's boyfriend. Miss Havisham is glad that Estella has broken Pip's heart. Steve becomes saddened to know that Estella was using him to hurt Pip. Miss Havisham explains that she has Estella break men's hearts to use their tears to power her "Genesis Device". Miss Havisham desires youth and wants to use the device to switch bodies with Estella. She then uses robot monkeys to attack Pip. Pip escapes and falls unconscious, awakening at an old house with Joe and Pocket. The anonymous person who sent Pip to London is revealed to be the escaped convict Pip met at the beginning of the story. Because of Pip's kindness, the convict led a life of goodness and became a millionaire. Sending Pip to London was his way of repaying Pip for the good that Pip did for him. The four of them, Pip, Joe, Pocket, and the convict, decide to stop Miss Havisham.
The group returns to the mansion discovering a bunch of men with broken hearts and a Miss Havisham powering up her device. The convict is killed by an acid-spewing Miss Havisham in the struggle, and Joe is overwhelmed by the robot monkeys. Pocket tries to get the broken hearted men not to cry, so they won't power the Genesis Device. His attempts at distracting them however make them feel even sadder. Pip tries to convince Estella to leave the machine. Pip reaches into a sack and pulls out a bunny stating that no one with a heart would kill a bunny. He gives Estella the bunny and she breaks its neck. Pip then continues to pull out bunnies, with Estella killing each one, until they get to the twenty-sixth bunny. Estella doesn't see the point in killing the bunny and Pip says to Estella that her not killing the twenty-sixth proves that she has a heart which gets her to leave the machine. This destroys the machine and sets Miss Havisham on fire. Joe, Pocket, Estella, and all the men with broken hearts leave the mansion. Estella finally declares her love for Pip, after which Pocket asks for his bunnies back.
The episode ends with the British Person closing the episode declaring: "Then they all live happily ever after, except for Pocket, who died of Hepatitis B."