When Homer accumulates gambling debts, Fat Tony asks to use the Simpsons home to shoot an adult film. When Marge comes home and sees the film being made, she leaves Homer and the kids. Marge encounters Caleb Thorn, a scientist with the passion for saving the endangered manatee. Homer and the kids drive off to find Marge and stop off at their country cousins house on the way. When they locate Marge, Homer decides the only way to get Marge back on side is to save a herd of manatees from a jetski gang. But when his mouth gets the better of him, the gang ends up beating Homer to a pulp. His cousins save him and Marge tends to the wounded Homer. She decides the only endangered species for her is her devoted husband. The family takes a vacation and Homer hires a manatee to fill his position at the power plant.

The family are awoken by loud construction noises next door, where a new stamp museum is under construction. The family lead a protest to stop the production of the museum in their residential area, and instead the stamp museum is moved to the site of the Springfield Cemetery. The cemetery is relocated next to the Simpsons home instead. Lisa's room has a view overlooking the graveyard which leads her to sleepless nights, running to Homer and Marge's bed for comfort. They try to show her there's nothing to be afraid of by spending the night in her room but they're also scared back to their own room. When a psychiatrist offers them some costly advice which they avoid, Lisa decides to spend the night in the cemetery to conquer her fears. She is knocked unconscious and suffers a hallucination where some storybook characters help her deal with her fear.

With Maggie displaying a rash, Dr. Hibbert informs the family that she has chicken pox. After Flanders suggests bringing his kids around to get infected, Homer & Marge throw a pox party to infect children who haven't had the disease. When Kirk and Luanne Van Houten find themselves at the party together, they get drunk and rekindle their love for one another. Milhouse thrilled with his parents getting back together soon realizes they're no longer competing for his love. Milhouse and Bart devise a plan to get them to split up again, by placing one of Marge's bras in the Van Houten bed. When Luanne discovers it she tells Homer, who abruptly accuses Marge of sleeping with Kirk. Bart confesses he was behind the prank but Marge kicks Homer out since he didn't trust her word. Bart puts his life in danger to get Homer and Marge back together which turns out to work.

Bartificial Intelligence: After Bart jumps from the second storey of their home, he is put into a coma from which he'll never emerge. Homer and Marge purchase an artificial robot boy named David to replace him. But when Bart wakes up from his coma the two boys try to compete for their mother's love, leaving Homer abandoning Bart in the woods.
Survival Of The Fattest: Homer and a group of his friends are invited to Mr. Burns' estate for a round of hunting. Little do they know they are the ones being hunted, by Burns himself.
I've Grown A Costume To Your Face: It’s the Springfield Semi-Annual Halloween Party but the costume contest goes awry when a witch turns everyone into real-life versions of their costumes. Lisa, as Einstein, searches for a solution to their problem; but it is up to Maggie, who was dressed as a witch, as the only one with the power to reverse the spell.

The family visits Paradise Pier as it's being dismantled. Homer purchases a dumbbell while Marge buys a tandem bicycle. When they arrive home Marge finds that nobody wants to ride the tandem bike with her so she rides it alone. Bart's friends notice and suggest that she's lonely, so Bart feeling sorry for her decides to ride with her. The two ride to a teahouse where they sit and talk over tea and cakes. The tea house closes the next day, prompting Bart to set up his own in his treehouse. Marge helps him decorate. When Bart is labelled a mama's boy, he rebels, breaking the redecorated treehouse as well as Marge's heart. Bart feels guilty so he suggests he and Marge sing a duet at the school's karaoke night. But when Marge witnesses Skinner and his mother's "mama's boy" antics she puts a stop to their newfound friendship to prevent Bart turning out like his principal.

It's fathers day, and when Bart purchases Homer a multi-function knife, Lisa decides to make her gift more personal. But when Homer doesn't appreciate her hand-drawn daughter-loves-father story, she rampages out of control, to the point where Skinner calls Homer and Marge into school for counselling advice. Homer decides he must win back his daughter's love, becoming the school's new "Safety Salamander". Meanwhile, Bart steals a street sign displaying his name to impress the bullies. This leads to a multi-car pile up, where Homer as the salamander rescues people from their cars. The pile up results in public scrutiny of Mayor Quimby and a recall election which most Springfield residents campaign for. Lisa decides with Homer's salamander suit, he could run for mayor and she could be his manager. But when his suit is destroyed the townspeople decide Homer's not worth listening to but Lisa is proud of him for trying anyway.

The mayor's estate is used for Springfield's Easter celebration, and in the course of the events, Homer embarrasses Marge in front of some new potential friends. To make it up, Homer decides to find her some new friends, with little luck. Marge finds some new friends on her own, Tammy and other members of "The Cheery Red Tomatoes," a group of women of a certain age. This group has plans for a fund raiser; they intend to rob Mr. Burns of 1 million dollars, an amount he once promised to charity. Homer finds out about the plan and tries to stop her from doing something she'll regret. Meanwhile, Lisa in search of summer opportunities decides to spend the summer in Rome. Lisa tells Principal Skinner that she speaks fluent Italian, since she really doesn't she tries to take a crash course and winds up hiring a tutor that turns out to be Milhouse.

Mr. Burns gets Homer and his family to collect his new car from Italy. Once there, the family decide to do some sightseeing and the car ends up totalled. Staying in the town they're stranded in, they discover Sideshow Bob is the English-speaking mayor who can help them. Bob tells the Simpsons how he came to be the mayor and introduces them to his partner Francesca and son Gino. Sideshow Bob offers to fix the car but in return they must keep his sordid past a secret. At their farewell party, Lisa drinks some wine and spills the beans about Bob which leads him and his family chasing them around Italy in a vendetta. The Simpsons seek Krusty's help, who is in Rome performing a comedy act. They put on costumes and hide in his show but they are caught out. Bob takes the stage with his family surrounding The Simpsons. Krusty arrives in his limo to save the day.

The First D'oh-el: Homer leads a sermon and tells the story of the first Christmas, with Marge as Mary, Homer as Joseph, Lisa as the angel Gabriel, Mr. Burns as King Herod, and Bart as Jesus.
I Saw Grampa Cussing Santa Claus: Grampa tells a World War II story in which he and Mr. Burns accidentally shoot down Santa Claus' sleigh while stranded on a desert island at Christmas.
The Nutcracker... Sweet: The lives of the residents of Springfield are visited at Christmas and Homer rushes around to get Marge a last minute present, to the tune of songs from The Nutcracker.

After a road accident caused by Marge results in the height of the Springfield Tire Fire increasing, the snow on Mount Springfield begins to melt, uncovering a frozen mailman from 1966. His mail is delivered, including a letter from Mona Simpson uncovering a secret affair and putting a question mark over the identity of Homer's true father. Homer tracks down the man from the letter, Mason, who invites he and his family onto his private ship. The family love him, but Abe feels betrayed. After a DNA test it is revealed that Mason is Homer's father. Mason takes Homer on an underwater treasure hunt, but when Homer is caught in coral and comes close to death, he remembers the fun times he had with Grampa. In hospital, Grampa reveals that he is his real father because he switched the DNA samples after he saw how happy he was with Mason.

Bart and Milhouse mess around in the school's steam tunnels, leaving the school destroyed. Skinner suggests Bart be sent to a behavior modification camp to set him straight. Homer takes Bart to the airport but discovers at the last minute that Bart has been banned from flying on airplanes. Homer must instead drive Bart to the camp, meaning he'll miss out on a trip to Las Vegas with his bar friends. Bart escapes the road trip by exiting through the bathroom window at a nearby diner, leading Homer to duct tape and chain him to the car seat. When they arrive at camp, Homer decides to skip the camp and takes Bart to Vegas with him. Homer and Bart get in trouble with the law, leading them to be thrown in prison. Meanwhile, Marge is also imprisoned for selling prescription drugs illegally at a yard sale, leaving Lisa and Maggie home alone.

A substitute gym teacher arrives at Springfield Elementary to cause Bart grief with his bullying. Bart exacts revenge by filling a dodgeball with ice and throwing it at the teacher, but he ducks and the ball instead destroys Willie's shack. Marge apologises for Bart and offers to let Willie stay with them. Lisa spends time with Willie, and decides she could turn him into a proper gentleman for her school science fair. Meanwhile, Homer rips his last pair of blue pants and discovers they are no longer produced. This leads Homer to start a "buy blue pants" advertising campaign which is seemingly successful. Lisa finally gets Willie to act sophisticated, and she wins the science fair. Willie however misses his old life, so he undoes his changes and moves back into his repaired shack.

While visiting a cave, the family are thrown into a hidden cavern below the main tour with Homer stuck in a narrow hole. Marge and Bart split to find an exit, while Lisa keeps Homer company by telling him a story. It begins a week ago, with Lisa chased into Burns' attic by a goat, where she discovers a photo of Burns employed at Moe's. This leads Burns into a story within a story, in which he was in a scavenger hunt with all his posessions up for grabs. Burns lost and had to work for Moe to make up the money. Burns tells Lisa of another story told by Moe, about hidden treasure and a fling with Mrs. Krabappel. All stories come to a dramatic end in the present time, where the hidden treasure in Moe's story is located in the cave. The Simpsons, Rich Texan, Mr. Burns, and Snake have a dramatic standoff but the treasure is destroyed.

Ned Flanders wins a computer and offers it to Marge, as he has no use for it. In return, Marge babysits Rod and Todd. With Marge spending so much time at The Flanders', Homer must look after Bart and Lisa. Meanwhile, Marge takes Rod and Todd to a children's activity center as she feels Ned is overly worried about his sons. Rod climbx a wall and discovers a new activity he enjoys, but he falls and suffers a minor injury. Ned is shocked and tells Marge to stay away. Homer takes the kids to an animal retirement home, but the trip goes awry when Toot-Toot the monkey pulls Bart into her cage and holds him hostage. Marge learns of the kidnapping and tries to get her son back. The monkey takes Bart atop the church. Rod, putting his new climbing skills to use, climbs the church to rescue Bart. Ned discovers that as long as Rod has his encouragement he will succeed in life.

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.

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.

As the family waits for their food at "The Frying Dutchman," they pass the time by telling stories.
Lisa's Story: 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's Story: Bart recounts the story of Mutiny on the Bounty featuring Skinner as Captain Bligh and Bart as Mr. Christian.
Homer's Story: 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.

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.

Marge goes on a cleaning frenzy before the housekeeper she’s won the services off 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.

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.