NOTE: This spoiler was sent in by jackcooldude666 (yeah, that's his name)
The movie begins in space. A space shuttle lands on the moon. Scratchy, the cartoon cat, climbs out and meets up with Itchy, the cartoon mouse, who then proceeds to attack Scratchy with the flag, and then takes off back to Earth, leaving Scratchy to die. Back on Earth, Itchy is declared a hero and eventually becomes President. One day, he sees Scratchy (still wounded) on the moon through a telescope, who threatens to tell everyone. Panicking, Itchy decides to send millions of rockets to the moon to kill Scratchy, which he does. The rockets go into Scratchy's body and the extra pressure from a single rocket makes him explode... which is when Homer Simpson's head appears in the middle of the action. We then see that the entire Simpson family is in the local theater watching Itchy & Scratchy. Homer then goes on to say that "people who pay to see something they can watch on TV for free are suckers... especially YOU!" [Points at audience].
After a little montage of life in Springfield, we cut to Green Day, who are performing on a stage floating in the Springfield Lake. They're playing the Simpsons Theme Tune, and everyone joins in. However, they start to talk about the environment, and the crowd throws their beverages at them in outrage. Only Lisa (who is present) listens to them. The garbage thrown by the crowd gets into the lake, and the stage begins to disintegrate The ship sinks (a la Titanic), drowning Green Day in the process.
We then cut to the Church, where a funeral service is being held for Green Day (the organist is playing "American Idiot - Funeral Version"). The Simpson family arrive late for church. During the service, a bright light shines upon Grampa Simpson, who then proceeds to have a fit, warning others of the things to come, including a "curly tail" (I think), being "trapped forever" and the syllables "ee-pa". Comic Book Guy records this fit on his cell phone (important later). Homer rolls Grampa up into the church rug, and take him home with them. On the way home, Marge becomes worried about the things that Grampa said. When the family stop for waffles, Marge gets out and walks home.
At home, Comic Book Guy has shown Marge the video of Grampa on his cell phone. She puts together words on the refrigerator that match Grampa's exact words. Meanwhile, Homer has been given a list of chores to do. One of them to get rid of the sink hole in their back yard. Homer solves this by putting Maggie's sandbox over the sinkhole (important later). Later, Homer and Bart are on the roof, fixing it. Bart suggests they do a dare contest to make things more fun. After a couple of dares (and a surprise advertising message from Fox), Homer dares Bart to skateboard to Krusty Burger and back... in the nude. Bart accepts this dare, and is soon full frontal and on his skateboard (NOTE: you will see Bart's genitals in this see, so be warned). It's a funny scene, especially when a naked Bart skateboards past Ralph Wiggum, who then says "I like men now!". However, just as Bart is about to reach KrustyBurger, the police shoot him off his skateboard which sends him flying onto a window at the fast food restaurant. Bart is then handcuffed to a lamp-post by the police. Homer then arrives and (in order to avoid being blamed for Bart's streak, which would send him to parental guidance counsellors) says that it was all Bart's idea. Although Homer gives Bart some clothes to wear (sans his pants), Bart is gutted to have a father who doesn't seem to care for him.
Ned Flanders, who is in KrustyBurger with his sons, gives Bart some pants to put on, which Bart is grateful for. Meanwhile, Homer spots Krusty the Klown, who is filming a new commercial opposite a live pig. After the commercial, the pig is about to be killed when it runs over to Homer, puppy-dog eyes and all. Homer decides to take him in. At home, Homer introduces Marge to the newly-adopted pig, when she realizes that the pig is the "curly tail" from Grampa's fit. She wants it to go, but Homer ignores her and keeps the pet for his own.
Meanwhile, Lisa is going from house to house to spread the word about the environment, only for her to be shut the door on. However, she meets another person doing the exact same thing, and it's love at first sight (for Lisa, at least). His name is Colin, an Irish boy whose father is a musician (it's not Bono). Lisa is in love (awwwww...)
Back at home, Bart is sitting on a branch looking on at Homer playing with his new pig, feeling neglected. He then stares over at Flanders' kids' bedroom. He sees that Flanders is a much better father to his boys than Homer is to Bart. Flanders, who has noticed Bart on the tree, invites him to go fishing the next day. Bart eventually agrees.
Meanwhile, Lisa is in the town hall, giving a talk about the environment (cunningly titled "An Irritating Truth"). Colin plays during this talk, and Lisa gets a little distracted. Nonetheless, she gets her message across to Mayor Quimby, who then orders the citizens of Springfield to stop dumping their stuff into the lake.
At the lake, Ned and Bart are fishing peacefully. When Bart accidentally loses Ned's fishing rod, he is amazed that Ned doesn't strangle him like Homer did. Speaking of Homer, our lovable oaf is confronted by Marge, who asks about where the pig's bathroom is. He shows her a silo filled with pig faeces, to which Homer, apparently, contributed to. Marge tells him to get rid of the excrement properly, which leads to Homer, in his car with the silo attached to the top, in line to drop the silo off at the waste disposal. He gets a call from Lenny, who tells him that they're giving away free donuts. Homer, impatient with the queue and wanting some of those donuts, speeds off and arrives at the lake. Unaware of the many signs saying not to dump in the lake, Homer does just that with the silo. He lets the silo (with all its literal crap inside) float down into the water, which causes the lake to turn black. After Homer drives off, a squirrel jumps into the lake and comes out all mutated with multiple eyes.
Bart and Flanders take a hike across the Springfield hills when they encounter the mutated squirrel. Suddenly, from out of nowhere, officials from the EPA (Environmental Protection Agency) take it away. We then cut to the White House, where the head of the EPA, Russ Cargill (voiced by Albert Brooks), tells the President, Arnold Schwarzenegger (who looks a lot like Ranier Wolfcastle) about the environmental crisis in Springfield. He is given 5 options to choose from, all in written form. Following his motto, "I was elected to lead, not to read", he spontaneously chooses Option No. 3.
We then learn that Option No. 3 was to seal Springfield in a big, glass sphere. Helicopters arrive and place the dome around the city. Every citizen in Springfield is trapped inside, including the Simpsons. Cargill appears before them via giant screen and tells them of the current situation. Homer and the pig try to act natural to avoid detection.
The townsfolk try to break out, but to no avail. Marge is at home when she notices that Maggie has somehow gotten outside of the dome. When she brings Homer out to see, Maggie is back in the sandbox. Marge thinks that she has gone crazy, but we soon learn that, thanks to the sinkhole under the sandbox, she can sink into the sand, and appear from another sinkhole on the other side.
That night, Homer and Marge watch the news, when they discover that the source of the contamination has been found: the pig silo. Marge is furious that Homer didn't listen to what she said to do. However, an angry mob who had also watched the news come after him with torches. Lisa is also furious with Homer. The mob forces its way into the house and it looks like they are all doomed. Ned Flanders, thankfully, tries to get the Simpsons across to his house on a board, but the pig makes it fall off and the Simpsons make a run for the car. Marge goes back into the house to get the video of Homer and Marge's Wedding. It seems that they are speeding away, but the mob has gotten hold of the car and are now leading it to five pieces of rope, meaning they are to be hanged. Marge, Bart, Lisa and Maggie make it to the treehouse, but Homer has gotten stuck in the noose. After unsuccessfully trying to reason with the mob, they start to shake the tree, trying to get the rest of the family out. Maggie then jumps into the sandbox and appears on the other side of the dome. The rest of the family follow her lead, including Homer, who takes longer to sink than the others. After Homer disappears, the sinkhole grows larger and eventually destroys the Simpsons' house. After the Mob leave the ruins of the house, Colin (Lisa's crush from earlier) comes up to Lisa who is on the other side of the dome, and starts to play her a song he wrote. The EPA soon arrive to search for the Simpsons, and they flee. (It should be noted that the pig seems to have buggered off from now on, which leads me to believe that he must have been eaten by the mob).
The Simpsons, now on the run, make it to a motel where they share their disgust with Homer (except Bart, who has passed out drunk after drinking the whisky in the mini-bar), but Homer has a solution: they go to Alaska and start a new life there. After getting the family to get involved with his idea, they win a truck at a carnival after Homer successfully rides a motorcycle around a spherical object without falling off (important later).
Meanwhile, back in Springfield, the conditions grow worse. There are rolling blackouts occurring every so often. Dr. Hibbert, Chief Wiggum and Apu try to persuade Mr. Burns to supply the town with power, or he'll release the hounds. He does the latter.
The Simpsons finally make it to Alaska, where the scenery is exactly as Homer pictured it. They buy a small wooden house and begin their life anew. In one funny scene, Homer and Marge undress for sex, with the help of various animals (taking the piss out of Snow White).
Back in Springfield, a desperate city can't take the conditions any longer, and try to break down the dome. It just so happens that Cargill is showing these attempts to break out to President Schwarzenegger. He displays another set of written options, and gets the President to pick Option No. 4: Destroy Springfield.
In Alaska, the Simpson family watch TV and see a commercial for a new type of Grand Canyon, which is exactly where Springfield is. It should be noted that the commercial is hosted by none other than Tom Hanks. Anyway, Marge realizes that the EPA plans to blow up Springfield in order to create this new Grand Canyon. The family decide to save Springfield, but Homer selfishly says that they should stay in Alaska, where things are much better. Bart then says to Homer that he thinks that Flanders was a better father figure than Homer ever attempted to be. He storms out after hearing this, goes and gets drunk at a bar, hitches a ride back to the chalet to find that it is empty. He finds a video on the bed, instructing Homer to play on the VCR. It is a message from Marge, saying that her, Bart, Lisa and Maggie have gone back to Springfield to save it from disaster, and aren't coming back to Alaska. To prove that this really is goodbye for good, Marge has taped over the video of Homer and Marge's wedding to record this message. It then switches back to the wedding, which shows a newly-married Homer and Marge happy together. An upset Homer leaves the house, passes out, falls down a cliff onto a piece of ice, which then breaks off and forms the shape of a heart. It slowly breaks in two as an unconscious Homer drifts on.
To be continued... immediately!
A polar bear is examining a still unconscious Homer when a mysterious woman scares it away. She then drags Homer to her hut where she revives him and makes him do a weird ritual until he has an epiphany. Soon enough, he has one, and the epiphany is that he is unhappy because of his abandonment by his family, and in order to make himself happy, he must save Springfield and his family. He thanks the mysterious lady and hitches a ride on a dog sled. However, after a montage of abuse, the dogs attack him and desert him. Luckily, the spirit of the lady appears before him and she points him in the right direction with her boobs.
Meanwhile, on the train to Seattle, Marge, Bart, Lisa and Maggie are overheard on their plan to go to Seattle and tell everyone about Springfield by the government. At the Seattle train station, Cargill and his henchmen capture them and place them in an armored truck.
Homer, meanwhile, has somehow gotten back to Springfield and starts thinking of ways to save the town. He hears Lisa's saxaphone playing in the armored truck, leading him to see it approach Springfield. He then sees a crane with a big ball on it and gets an idea. He makes a sign saying "SOP" instead of "STOP", and while this distracts the drivers, Homer drives the big crane to the armored truck and tries to free his family (which, if you've seen the trailer, ultimately fails). The Simpson family are put to sleep from knockout gas.
They awaken to find themselves back in Springfield, which is now destroyed and overrun by savages. Cargill appears on the screen to tell the remaining townsfolk that Springfield will be destroyed by a bomb that will go off in 10 minutes. On the outside, Homer knocks out a guard and attempts to climb to the only entrance/escape to the dome: a circle at the top.
In Springfield, the townsfolk try to escape to the exact same place by using the rope that is attached to the bomb. However, Homer makes it to the top first and just as the townsfolk are about to make it to the top, Homer slides down the rope, knocking various citizens off the rope on the way. The rope breaks and the bomb and Homer fall to the ground. Bart tells him that he's doomed them all... again. When Homer inadvertently makes the bomb go off in less time, he is hated once more. When all seems to be lost, Homer finds a motorcycle and gets an idea. He takes the bomb with him on the motorcycle and finds Bart, who is at church praying with the Flanders. After Homer tells Bart how he will take much better care of him, he refuses to ride with Homer, but is won back after Homer tells him that he can hold the bomb. The pair have the bomb with them and try to throw it out of the dome. They successfully do this, mere seconds before it explodes. It destroys the glass dome, bringing air and delight to Springfield once again.
Russ Cargill approaches Homer and Bart, aiming at them with a gun. As he is about to shoot, he is knocked out from a rock knocked onto his head by Maggie.
Lisa tries to find Colin, which she does despite Millhouse telling her that he was dead (another attempt to win Lisa over). They walk hand in hand to clean up the Springfield Lake.
Homer and Bart arrive back in Springfield safe and sound, to learn that no-one was hurt when the glass was shattered (except Dr. Nick, who was crushed to death by the glass). Homer sees Marge in the distance, and sweeps her off her feet onto the motorcycle and they drive off into the distance. Their house is also rebuilt.
NOTE: Clare adds the following to this spoiler...
There are several extra clips throughout the cedit sequence:
At one point seats can be seen and the Simpson's appear discussing why they are watching the credits. As they get up to leave Marge tells them that she thinks Maggie is going to say her first word which turns out to be "sequel".
At the very end of the credits seats appear again to show a cinema worker moaning that he spent so many years at film school to mearly sweep up the rubbish and that being assistant manager is not all its cracked up to be.
*CUT TO THE CHASE*
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Homer, Marge, Bart, Lisa and Maggie Simpson discover a plot to destroy Springfield to make way for a new Grand Canyon. They go back to a quarantined Springfield and prevent the disaster from happening. The iconic Simpsons house, which was destroyed earlier in the film, is rebuilt.
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