Marge is outraged when she discovers Homer allowed Fat Tony to shoot a "gentlemen's" film in their house to make restitution for his football gambling debt. So she takes off and leaves Homer with the kids. While on her journey of self-discovery, Marge befriends Caleb Thorn, an attractive marine biologist who is on a quest to save not only the endangered manatee, but Marge from a husband who doesn't seem to appreciate her.
After protesting the construction of a stamp museum scheduled to be built on their neighboring lot, the Simpsons are dismayed when they discover that what they thought was a successful relocation of the museum to a cemetery lot turns into a creepy nightmare when that cemetery moves next door. When Lisa's sleepless nights become too much for Homer and Marge, they turn to a psychiatrist for advice. Meanwhile, Lisa chooses to face her fears dead-on by visiting the cemetery alone late one night.
Homer capitalizes on Maggie's chicken pox by throwing a "pox party" and charging parents to infect their children. Meanwhile, Milhouse soon realizes he was better off when his parents competed for his love, and launches "Operation Reverse Parent Trap" .
It's time for all-new tricks and devilish treats on THE SIMPSONS annual Halloween trilogy, -Treehouse Of Horror XVI.- The fright-fest begins in - B.I.: Bartificial Intelligence - when the Simpsons adopt David, a newly developed artificial robot son, to replace Bart after he falls into a coma. In - Survival of the Fattest,- Mr. Burns invites Homer and his friends to his gigantic estate for a hunting tournament, but Homer and the gang learn they are the ones being the hunted on -The World Series Of Manhunter- hosted by Bradshaw. In the final Halloween scare, -I've Grown a Costume on Your Face,- a costume contest goes awry when a real witch turns all the Springfieldians into real-life versions of their costumes, leaving Maggie dressed like a witch with the only real power to reverse the spell.
Observing that Marge is lonely, Bart offers to spend time with her. After they go on tandem bike rides and decorate Bart's tree house as a teahouse, the bullies from school dub Bart a mama's boy. When Marge finds out that Bart's schoolmates are teasing him, she gives him the necessary tools to win back his reputation. Meanwhile, Homer teams up with Moe and joins a professional arm-wrestling circuit .
Homer's inability to embrace Lisa's Father's Day book the same way he does Bart's Father's Day Toolman causes Lisa to develop Ddd. Meanwhile, Bart steals the Bart Boulevard street sign and causes a huge pile-up. While Mayor Quimby creates The Safety Salamander spokesperson in response to the accident, the town still forces the ineffective Mayor into a recall election. Homer, longing to win back his daughter's love, takes the spokesperson position, and after a heroic run as The Safety Salamander, he runs for Mayor along with every other unqualified Springfieldian.
Homer has an altercation with the Easter Bunny at the Mayor's egg hunt, causing Marge to be shunned. A 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 - who turns out to be Milhouse.
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 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.
The Simpsons deliver holiday cheer in this Christmas-themed trilogy. In The First -El, - when Reverend Lovejoy's car breaks down en route to Christmas mass, Homer takes over the sermon and delivers his version of the birth of Christ to his parents Joseph and Mary. - I Saw Grampa Cussing Santa Claus - finds Grampa reminiscing about his daredevil days as a WWII fighter pilot, when he was stranded on an island alongside his gunner, Burns. Grampa recalls mistaking Santa Claus for an enemy aircraft and gunning him down from the sky. Realizing their mistake, Grampa helps Jolly Ol' St. Nick to safety, only to have Burns steal the sleigh and escape the island - leaving Grampa stranded again. The final installment, -The Nutcracker - Sweet,- which finds the townspeople of Springfield preparing for Christmas Day, is set to the tune of the famed Nutcracker ballet.
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 a key from Principal Skinner's office and gets himself into hot water, 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.
The Simpsons open up their home to Groundskeeper Willy after Bart accidentally destroys his house. But soon after his arrival, Willy's poor manners become the focus of a bet between Bart and Lisa, as she takes on the challenge of turning him into a proper gentleman. Meanwhile, Homer rips his favorite blue pants and starts an ambitious advertising campaign to reestablish the discontinued garment.
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's obsession with Lenny's new plasma TV prompts Marge to enter the family in a sweepstakes, and they win a trip to the Fox Studio Lot. Against Marge's wishes, Homer signs them up for a "Trading Spouses"-type show and is forced to take in a controlling wife, while Marge moves in with a beaten-down husband, Charlie, and his perfect son. Charlie quickly develops a crush on Marge, while she tries to give him the strength to stand up to his own wife.
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, 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.
When the Simpsons' plans for a nice family outing at the Frying Dutchman turn into a dining disaster, the family tries to salvage the night by telling different stories of disasters at sea. Lisa recounts the Mayflower voyage, Bart tells tales of Tahitian mutiny and Homer puts his own spin on the 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, 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.
After visiting an evolution exhibit narrated by guest star Griffith, Flanders pushes Mayor Quimby to appoint Reverend Lovejoy as a "Mortality Czar" in charge of spreading the theory of creationism. Darwin's theories are quickly outlawed and Lisa finds herself as the only supporter of the scientific theory. After holding secret evolution classes, Lisa is arrested and retains Southern lawyer Wallace Brady to help defend her beliefs in front of a judge. While Flanders is on the stand in court, Homer's antics cause him to crack under pressure and he calls Homer an ape, which leads the judge to believe Homer resembles the missing link - putting a monkey wrench in the prosecutors' case.
After a passionate kiss between Marge and Homer airs on the Isotope Jumbotron, struggling second baseman Buck Mitchell turns to the couple for marital advice. The Simpsons are able to get Buck and his sexy singing wife, Fiona, on track, and the Isotopes' season turns for the better. Things seem to be coming up aces for the Simpsons until Buck catches Homer giving Fiona a post-show neck massage, which results in both couples separating.