"Bart's Comet" is the fourteenth episode of Season 6.
Springfield's days are numbered when Bart discovers a comet is heading straight for them. Now they must choose who will brave the comet's arrival and who can stay in the Flanders' bomb shelter.
After vandalizing the school's new weather balloon, Bart, as usual, is considered the chief suspect. Bart's guilt is proven when he carelessly kept the plans of his mischief in his pockets. As a result, Bart is punished by being made to awaken at the early hours and having to help Skinner while he goes sky watching. Skinner hopes to find something which he could have named after himself; however, he spots the balloon and leaves briefly to try and catch it, telling Bart not to touch the telescope. Bart messes with the telescope; after flailing the scope around on its tripod, Bart looks through it to discover a comet outside the Earth's atmosphere, much to Skinner's dismay.
Bart's discovery makes the papers and he becomes famous among the nerds at school. However, when Bart is requested to show a group of students known as the Superfriends the comet, he directs them to the window, as the comet is seen in full daytime. The Superfriends realize that something is wrong with it. Lisa also attempts to warn Bart and explain that the comet is most likely heading for Earth, and is going to decimate the town. These fears were confirmed when they alerted the Springfield Observatory of this new development, and they analyzed it through their telescope. Homer comforts his family by saying that the comet will just burn up in the atmosphere and become a rock the size of a Chihuahua's head.
Springfield officials plan to launch a rocket at the comet, leading to relief and arrogance among the townfolk. Instead of leaving town like they should Springfielders stay to watch the rocket, but it misses and blows up the only bridge out of town, leaving the townsfolk doomed. Later on, while watching the news, Homer tells the kids that the government wouldn't just leave them to die; it then cuts to the capital on the news where the evacuation is being discussed. It looks like the bill will go through and the town will be rescued; that is, until one congressman takes on a very unpopular amendment to the bill leading to its uninamous rejection, meaning the government will leave the town to get wiped out.
They all choose to go to a bomb shelter; however, the only one in town belongs to Ned Flanders, who is too nice to refuse them. The bomb shelter is too cramped and the door won't shut, so the inhabitants agree to evict Ned from his own shelter after discussing who would be unnecessary in the new world. To pass the time (and to drown out Ned’s singing of “Que Sera, Sera”) they play a guessing game, but this causes an argument. Feeling guilty about sending Ned to die, Homer leaves the shelter; the group of people abandon the shelter and join Ned outside waiting for the comet to strike and singing what he sang after being evicted from his bomb shelter; the townfolk join him in song. The comet hurdles towards Springfield, but starts to deteriorate upon entering Springfield's atmosphere (which is full of highly toxic pollutants), gradually shrinking to the size of a Chihuahua's head. It pops Skinner's vandalized weather balloon, which bounces off Ned's bomb shelter causing it to collapse (much to the distress of Ned and Moe), and falls towards the townsfolk, now harmless. Bart puts the remains of his comet into his pocket. All of Springfield's citizens then head to the Observatory to destroy the location so what just happened will never occur again. The epilogue features Bart, Lisa and Homer becoming petrified, because of what Homer mentioned regarding the comet literally came true, much to their surprise.