The family is on a nature walk through “Carl’s Dad Caverns,” when Homer tries to get a piece from a stalactite. This results in the family falling through the cave floor and winds up with Homer getting stuck in the ceiling of one of the lower chambers of the cave. Marge, Bart and Maggie go off to find help, while Lisa stays behind and tells her father a story to pass the time. Her story involves running from a bighorn sheep and into Mr. Burn’s mansion. The pair evades the tenacious sheep by finding refuge in the mansion’s attic, where Mr. Burns tells her the story of how he came to work at Moe’s Tavern by losing a scavenger hunt with a rich Texan. While there he learned (and tells to Lisa) the tale of the Moe’s treasure. The stories within stories culminate in the fate of the treasure being determined in the cave.

Marge goes on a cleaning frenzy before the housekeeper she’s won the services of comes to the house. One spot remains and she mixes a number of toxic cleaners together to tackle the job. The noxious mixture knocks her out and she wakes up suffering from amnesia. Marge is taken home and the family tries to bring back her memory. She starts to get back memories of her children and other insignificant things, but when it comes to remembering her husband, nothing he does seems to jog her memory. When he can’t get her to remember him, he tries to win her all over again, especially after Patty and Selma get her back out on the dating scene.

Working through their checklists of things to do before summer ends, Lisa gets the family to go a museum. At the Springfield Museum of Natural History there is an exhibit Lisa is excited to see on Women’s History turns into an exhibit on the history of weapons, which excites Homer and Bart. When Flanders sees the exhibit of evolution and another that mocks creationism, he raises an alarm. Reverend Lovejoy gets Skinner to have creationism taught in school. Lisa is the only one who holds onto the scientific theory. She brings the topic up at the town meeting and the town votes to teach only one theory, creationism. Lisa decides to hold her own class on evolution, until she is arrested. The ACLU gives her a lawyer who is up against a slick Southern lawyer, but ultimately it’s a family member that is a key to her defense.

After the family successfully protest against a stamp museum being built next to their house, a cemetery is built near the Simpson house instead, making the normally unflappable Lisa realize that someone as smart as her can be afraid of something.

Homer brings the whole family along when he is sent to Italy to pick up a new sports car for Mr. Burns, when they find themselves in a small town that Sideshow Bob has become the mayor of.

The Simpsons re-enact the Nativity; a World War II tale stars Grampa, Mr. Burns and Santa; a musical features "The Nutcracker Suite."

After Bart steals a key from Principal Skinner's office and gets himself into hot water, Marge and Homer send him to a behavior modification camp.

The family is at a church fund-raiser, where Homer tries to ensure his rubber duck onto victory, but Flanders wins the big prize, which he doesn’t want and gives it to Marge. In return Marge agrees to watch Rod and Todd while Ned is attending a left-handed convention. While Marge is spending all her time with the Rod and Todd and trying to let them learn how to be boys; Homer takes Bart and Lisa to a home for former celebrity animals and a monkey kidnaps Bart. Marge’s ability to be a mother comes into question when Ned discovers what she is doing with his boys and the local news covers Bart’s current predicament.

The family attends "Stab-A-Lot: The Itchy and Scratchy Musical." The musical's director is a graduate of Springfield Elementary and Principal Skinner puts his foot in mouth when he makes sexist comments about her education and that of women in general. He tries to make the situation better, but only buries himself deeper and deeper until he is fired and replaced by Women's Educational Expert Melanie Upfoot. The first thing she does is split the school into girls and the boys. Lisa dislikes the way girls are being taught math and she ventures over to the boy's side of the school in search of a challenge. Disguising herself as Jake Boyman she starts attending the boy's school but while she finds the math problems more interesting, it is being a boy that is a greater challenge.

Mail from forty years earlier is discovered, and a letter from Homer Simpson's mother's old boyfriend states that he is Homer's true father. Homer sets out to find his supposed new father, leaving Abe behind.

At the power plant a movie is shown where the workers endorse outsourcing and Mr. Burns announces that he is closing the plant and moving the work to India. Homer is the only union employee left on the payroll and he is sent to India to train the replacement workers, when he succeeds beyond expectations, he is given total control of the plant and declares himself a god. Meanwhile, Selma & Patty take Bart and Lisa to their MacGyver convention. When they discover Richard Dean Anderson doesn’t like MacGyver and much as they do, they kidnap him in retaliation. Anderson escapes only to enjoy the thrill and he turns himself back in so that he can escape again. When it happens over and over again, soon Patty and Selma are the ones who need a means of escape.

Bart ends up in a coma after attempting to jump from the roof to the swimming pool at Spinster Arms Apartments, while attending a hunting party at Burns Manor, Homer panics and believes the prey is the hunting party, and after losing a Halloween costume contest to Dr Hibbert as Dracula, a real witch puts a spell on the people of Springfield.

When Bart decides to spend a bit of time with Marge, it's not long before he's buying tea sets and singing duets. Has he turned into a mummy's boy?

Homer becomes Springfield's safety guru and before long he's challenging Mayor Quimby for office. Until, that is, there's an embarrassing mishap with his costume.

Marge is shunned after Homer has an altercation with the Easter Bunny at the mayor's egg hunt. A lonely Marge joins a women's group who plan to steal $1 million from Mr Burns.

When Homer hears that the Isotopes are on a winning streak, he takes the family to the game. The first baseman’s game is going bad, caused by his sexy singing wife Tabitha embarrassing him during the game’s national anthem. Buck Mitchell sees Marge and Homer’s kiss on the game’s Kiss-Cam and comes to them for marital advice. They start working with the couple and Buck’s baseball career turns around, but it and the Simpson marriage goes awry again when Buck catches Homer giving Tabitha a neck massage. While Marge and Homer try keeping their marriage together they also try to get Buck and Tabitha back together.

After Homer gets into trouble over his football gambling debts, he allows the Springfield Mafia to shoot a "snuggle film" in the house without Marge's permission. When she and the kids return home from a trip to "Santa's Village" and find production still going on, a furious Marge leaves for the beach and encounters a marine biologist named Caleb Thorn who has dedicated his life to saving manatees.

Never one to miss the opportunity to make a quick buck, Homer cashes in on Maggie's bout of chicken pox. He decides to host a Pox Party and charges parents to infect their children.

As the family waits for their food at “The Frying Dutchman,” they pass the time by telling stories. Lisa tells about the Mayflower’s journey to America, where Marge and her kids are Pilgrims and they are joined by a knave named Homer who joins their family to escape the authorities. Bart recounts the story of Mutiny on the Bounty featuring Skinner as Captain Bligh and Bart as Mr. Christian. Homer tells the tale of the maiden voyage of a cruise ship in the 1970s featuring of a ship that can’t flip over, which of course it does and the attempts of the survivors to get out of the ship alive.

Mr. Krupt is the school’s new gym teacher and introduces Bart and the kids to “BOMBARDMENT!” Bart’s attempt to get back at the new gym teacher results in the destruction of Groundskeeper Willie’s shack and the family takes him in. Lisa decides to make Willie the focus of her science fair project and tries to turn him into a “proper gentleman” with surprising results. Meanwhile, Homer has ruined his last pair of blue pants and attempts to generate interest in them so the manufacturer will start making them again.

Homer is stoked for a party, where Lenny shows off his new plasma screen HD TV. Three days later and Homer still hasn’t left Lenny’s apartment. Lenny eventually gets him to leave and Marge enters them in a contest where they can win a plasma TV of their own. They don’t win, but 3rd place gets them a tour of the FOX studios, where Homer learns about a wife-swapping show where he can win enough money to buy his own plasma TV. Marge agrees to appear and they exchange wives with the Heathbar family. Charles Heathbar winds up falling in love with Marge (who is giving him what he needs), while his real wife Verity finds Homer detestable.

Homer spearheads the effort to get pro-football to bring a new franchise to Springfield. The football commissioner, on his way to officially award the franchise, stops at the Simpson house where Grandpa (mistaking him for a burglar) attacks him. Springfield loses out and Abe becomes the town’s pariah. After trying and failing assisted suicide, Abe decides to live his life without fear and when the town decides to reuse their football stadium as a bullfighting ring, he volunteers to be the toreador. Ever the activist, granddaughter Lisa protests his new profession.