Marge, outraged after discovering Homer allowed Fat Tony (Joe Mantegna) to shoot an a "gentlemen's" film in their living room in compensation for his football gambling debt, flees, leaving Homer with the kids. While on her journey of self-discovery, Marge befriends Caleb Thorn (Alec Baldwin), an attractive marine biologist on a quest to save not only the endangered manatee, but Marge from a husband who doesn't seem to appreciate her.
When a new stamp museum proposes locating itself next door to the Simpson house, the family protests it. As a result, the museum decides instead to build on the former site of a cemetery... and the bodies get moved to a new lot on Evergreen Terrace. Thanks to the new neighbors, Lisa develops sleepnessness because of her constant fears. After numerous attempts to get herself to go to sleep in her own room, Lisa decides that she must confront her fear and spend one night alone in the graveyard.
After nine years (in the non-Springfield reality), Kirk and Luanne Van Houten reunite. However, dismayed that they will no longer compete over his love, Milhouse launches "Operation Reverse Parent Trap" with Bart to get them to split again. Meanwhile, when Maggie gets chicken pox, Homer tries to capitalize on it by throwing a "pox party" and charging parents to infect their children.
The sixteenth annual Novemberween trilogy. The opening sequence will feature Kang and Kodos accidently sucking up the universe in a vortex after trying to speed up the baseball season so the show can start. This year's tales:
"B.I.: Bartificial Intelligence": After Bart falls into a coma, the family tries to replace him by adopting a robotic son named David. "Survival of the Fattest": Mr. Burns invites Homer and other Springfieldians to his estate for a huntin tournament, only to soon find out they're contestants (read: hunting targets) on "The World Series of Manhunter," hosted by Terry Bradshaw (in a cameo). "I've Grown a Costume on Your Face": A witch turns the people of Springfield into living versions of their Halloween costumes, leaving Maggie as a witch and the only one who can reverse the spell.
Bart sees that Marge is lonely so he offers to spend more time with her, going on tandem bicycle rides and redecorating the treehouse as a "teahouse", until bullies from school find out and accuse Bart of being a "mama's boy". When Marge learns of this, she gives him the necessary tools to win back his reputation. Meanwhile, Homer joins Moe in a professional arm-wrestling circuit.
Mayor Quimby appoints Homer a "Safety Salamander" spokesperson in response to an accident caused by Bart's latest prank: stealing the "Bart Boulevard" street sign, causing a huge pile-up. Meanwhile, Lisa has beome disappointed in Homer's lack of interest in her, so Homer tries to win back her love by being the best Safety Salamander he can be. When the town forces a recall election on Mayor Quimby, Homer decides to step down from his spokesperson post and run in the race, against many other underqualified Springfield residents.
Homer is distanced from Marge when he gets into a fight with the Easter Bunny at an egg hunt. Feeling lonely, Marge decides to join a women's group called the Cheery Red Tomatoes and agrees to help with an upcoming charity drive – robbing Mr. Burns of his Faberge egg collection. Meanwhile, Lisa's plans to spend a summer in Italy hit a bump when she learns the first requirement is being fluent in Italian, so she takes on a teacher from a classified ad. To her surprise it turns out to be Milhouse. Lilly Tomlin guest stars.
After Mr. Burns crashes his Stutz Bearcat, he sends Homer and the family off to Italy to pick up his new fancy sport car. While on their Italian adventure, the Simpsons end up stranded in a small Italian village where a rehabilitated Sideshow Bob (Kelsey Grammer) reigns as mayor. Sideshow Bob impresses the Simpsons enough so that they keep his sordid past a secret until one of the family members, in a wine-induced state, spills the beans.
Marge's rage against the new toll road system somehow leads to the discovery of a frozen mailman and his 40-year-old mail. The letters are returned to the rightful recipients, including one to Grandpa Simpson's deceased wife, revealing a secret love affair and the real father of her baby, Homer. Confused and emotional, Homer finds Mason Fairbanks, his wealthy and much improved paternal dad, and happily establishes a father-son relationship with him while rejecting his surrogate father of 40 years. But soon Homer realizes that a DNA test doesn't necessarily tell who his true father is...
After Bart steals the key for the school's steam tunnels and triggers and explosion that destroys Principal Skinner's car, Marge and Homer send him to a "behavior modification camp." Homer is forced to cancel his much-anticipated trip to Las Vegas in order to drive Bart to the camp, but on the way there, Homer decides it's a great time to bond with Bart.
When Bart accidentally destroys Groundskeeper Willie's shack with a game of solid ice dodge ball, Marge takes in the homeless janitor. Lisa decides to offer Willie a better life by refining him for her upcoming science fair, and after an arduous regimen, she turns the curmudgeon into the talk of the town. Meanwhile, Homer fears changing trouser styles when he discovers the factory that makes his classic blue pants is going out of business.
While cave exploring with his family, Homer causes the cave to crumble and finds himself stuck upside down in the ceiling. Marge and Bart search for help while Lisa passes the time by telling Homer a story, which turns into a chain of narrated tales.
Ned Flanders wins a new computer that features guest star Sarandon as the "You've Got Mail" voice and he offers it to Marge, as he has no use for it. In return, Marge babysits the Flanders children so that Ned can attend the Left-Handed Convention, where he meets New York Yankees guest star Randy Johnson, who is selling left-handed teddy bears
With Marge spending so much time at The Flanders', Homer must look after Bart and Lisa. 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 when it is a breaking news report and she must figure out a way to get her son back.
Homer and Marge go on a "Wife Swap" reality show, to win a widescreen TV set. The other contestant, Charles (Ricky Gervais), goes on to escape his raspy-voiced matriarch of a wife. She goes to live with Homer and the kids and thinks they're monsters, while Charles finds new love with Marge and tries to woo her with a love song.
Grampa ruins Homer's plans to make Springfield the new home of a pro football franchise when he mistakes the Commissioner of Football for a burglar and the football stadium is transformed into a bull fighting arena. Tortured by threatening calls from his family and friends, Grampa seeks Manfred Manslaughter's help in committing suicide. When his plan fails at the last minute, Grampa gets a new outlook on life and decides to become Springfield's very own matador.
Homer learns that the nuclear power plant is being shut down and outsourced to India. After Homer is sent to train the new employees, he becomes power hungry in his new position of authority. Meanwhile, Selma and Patty meet their Hollywood heartthrob, MacGyver (Richard Dean Anderson), and kidnap him for their own obsessive worship. When Anderson discovers how exciting real-life drama can be, he refuses to leave until Selma and Patty devise their own plan to get him out.
A dinner at the Frying Dutchman which turns out something less than spectacular sets the stage for three tales: Lisa tells about the Mayflower's voyage to America, Bart describes mutiny off the coast of Tahiti, and Homer speaks about capsizing cruise ships.
Springfield is in an uproar after Principal Skinner makes a sexist comment at the end of an Itchy and Scratchy musical. Principal Skinner is replaced by Melanie Upfoot (Frances McDormand), a women's educational expert, who decides to divide the school into two different schools: one for boys, and one for girls. Studious Lisa soon becomes frustrated when she isn't learning anything from "girls' school." When the Principal refuses to allow her to take math at the boys' school, Lisa decides to dress up as a boy. While Bart teaches her the ropes of boyhood, Lisa wins the math award at the Student Achievement Awards and learns what it's really like to be a part of the "boys' club.
After a spring-cleaning frenzy and inhaling too many fumes, Marge suffers from retrograde amnesia. In an effort to bring back her memory, Homer takes her around town to re-familiarize her with her surroundings. Marge still has no recollection of who Homer is and puts herself back on the singles market. Not until she realizes that Homer is truly genuine at heart will she remember who he is and why she loves him.
Ned Flanders gets Mayor Quimby to appoint Reverend Lovejoy as Springfield's "morality czar" dedicated to the cause of promoting Creationism and stamping out Evolution; when Lisa refuses to accept this, she is arrested and put on trial in a rehashing of the 1925 Scopes Monkey Trial (where teacher John Scopes was arrested for violating a Tennessee law which forbade teaching that humans descended from other animals).
The Springfield Isotopes's star second baseman is having marital problems, so when he sees Homer and Marge kissing on the Jumbotron, he asks them for advice, but when Homer is later caught giving a neck massage to the player's wife, it's a twin bill of marital ill.