Plot:
While performing on Lake Springfield, rock band Green Day are killed when pollution in the lake dissolves their barge, following an audience revolt after frontman Billie Joe Armstrong proposes an environmental discussion. At a memorial service, Grampa has a prophetic vision in which he predicts the impending doom of the town, but only Marge takes it seriously. Then Homer dares Bart to skate naked and he does so. Lisa and an Irish boy named Colin, with whom she has fallen in love, hold a meeting where they convince the town to clean up the lake.
Meanwhile, Homer adopts a pig from Krusty Burger and names it "Spider Pig" (later "Plopper"). Homer seems to show more love for the pig than he does for Bart which causes Bart to reconnect with Flanders. Homer stores the pig's feces (and some of his own) in an overflowing silo which Marge tells him to dispose of safely. Homer takes the silo and Plopper to the dump to get rid of the waste, but during a line-up of safe trash disposal, he receives a phone call from Lenny, who tells him that Lard Lad Donuts has been shut down and free donuts are being given out. Homer grows impatient and instead dumps the silo in the lake, re-polluting it to an even more severe degree. Moments later, a chipmunk jumps into the lake and becomes severely mutated. Nearby, Flanders and Bart discover the chipmunk during a hike, and the EPA captures it. Russ Cargill, head of the EPA, presents five "unthinkable" options to U.S. President Schwarzenegger to keep the town's pollution contained; Schwarzenegger randomly picks option three, enclosing Springfield in a large glass dome. When the police discover Homer's silo in the lake, an angry mob of townspeople approach the Simpsons' home with pitchforks and torches and attempt to kill them, but the family escape through a sinkhole that leads to the outside of the dome. They find a room to stay in for the night and Homer tells them that he has a plan; flee to Alaska to start a new life.
The trapped citizens damage the dome over time and Cargill, not wanting news of what he has done to become widespread, plans to destroy Springfield. In Alaska, the Simpsons see an advertisement starring Tom Hanks, for a new Grand Canyon to be located on the site where Springfield is located. Marge and the kids want to go and save the town, but Homer refuses to help the people who tried to kill them. The family abandon Homer and leave, but are captured by the EPA and then put back into the dome.
After a visit from a mysterious Inuit shaman who saves him from a polar bear, Homer has an epiphany and believes he must save the town in order to save himself. As he arrives at Springfield to do so, a helicopter lowers a bomb suspended by rope through a hole in the dome. Homer climbs to the peak of the dome and descends the rope, knocking the escaping townspeople and bomb off. Homer takes the bomb and a motorcycle. After reuniting with Bart, they drive up the side of the dome and Bart throws the bomb through the hole, seconds before detonation. The bomb explodes, shattering the dome, freeing everybody. Cargill, angry for ruining his plan, arrives and is about to shoot Homer with a shotgun, but gets knocked out when Maggie drops a rock on his head. The town finally praises Homer, who kisses Marge on the motorcycle before riding off into the sunrise with her and Maggie. The townspeople begin restoring Springfield back to normal.

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