Homer tries to light a jack o' lantern, but catches his hand on fire, then his whole body, so he starts running around screaming. Then, the Treehouse of Horror VII comes up in blood. Finally, the family runs to the couch, but they die from the Grim Reaper, who decides to put his feet up and use Homer's corpse as a footstool.

Bart and Lisa hear strange noises coming from the attic one night and get curious about them. The next morning, they ask Homer and Marge about the noises. Homer and Marge tell them to never go up into the attic. Homer then goes up to the attic with a bucket of fish heads. The next time Homer and Marge are out of the house, Bart, Lisa, and Maggie go into the attic to see what's up there. They see what they think is a monster and get scared and flee. During this, the monster got out of its chains and seemingly escaped from the house.

When Homer and Marge return, Bart and Lisa tell them that something escaped from the attic. Homer and Marge then explain that Bart was a conjoined twin, and the other twin, Hugo, was found to be evil. They kept him locked in the attic whilst Bart got to live his life. Homer and Marge then call Dr. Hibbert and they all go to find Hugo, leaving Bart alone. Hugo then shows himself to Bart, having not actually left the house. Hugo takes Bart up to the attic so that he can sew him and Bart back together again, believing that they were better that way. Dr. Hibbert then enters the attic and knocks Hugo out. Dr. Hibbert then realizes that the scar on Hugo doesn't match him being the left twin, so that makes Bart the evil twin. Bart is then confined to the attic whilst Hugo lives with the rest of the family.

For Lisa's science fair project, she places a tooth in a tub with Buzz Cola to see the effect of cola on teeth. Bart then enters Lisa's room to show her his "science project", which is him using a balloon to give Lisa a static shock. Lisa then touches her tooth in the tub and transfers the static electricity into the tooth and cola. The next morning, Lisa wakes up to find that mold has grown around the tooth. She then uses her microscope to find that there is a tiny stone age civilization living in the mold.

The new microscopic beings start advancing at a very fast rate, eventually outmatching Earth's technology. As Lisa is studying her new life, Bart comes along and sticks his finger into the tub. This causes massive damage to the city and angers the people. They create spaceships and fly out to attack Bart in his sleep. Bart gets outraged at this and tries to destroy The Little Universe, but Lisa stops him. Bart tells Lisa that she won't be able to protect it forever and leaves. A shrink ray is then used from The Little Universe and hits Lisa, shrinking her down.

The people of the city introduce themselves to Lisa and worship her as their god. They are then shocked to find out that Bart, who they refer to as the devil, is Lisa's brother. When Lisa asks to be grown again, the people tell her that they can't do that. Bart then comes back and takes The Little Universe and submits it as his own science project, winning the science fair. Lisa gets annoyed as she should have won the gift certificate then demands that her people bring her some nice shoes.

When Homer is out fishing one day, he is abducted by Kang and Kodos, who demand Homer takes them to his leader. Homer tells Kang and Kodos about the presidential election, which means there might be a new leader very soon. The Rigellians then set out to kidnap both Bob Dole and Bill Clinton, who are running in the election. After trapping the candidates in tubes, Kang and Kodos take on their identities and take over their lives. They then spray Homer with rum, so nobody will believe him, and dump him out of the spaceship. Homer returns home and tells his family what happened, but nobody believes him.

Kang and Kodos continue the election campaign together, giving promises and doing things that confused people. On the day of the election, Homer found the UFO and woke up Clinton and Dole. When trying to free them, he accidentally took the UFO into space and ejected them, killing the candidates. Homer then returns the UFO to Earth, crashing it into the United States Capitol. Homer then unmasks Kang and Kodos, revealing that he was right all along. The Rigellians are unaffected, telling the people that America has a two-party system and they have to vote for one of them. Eventually, Kang wins the election and becomes president and the Rigellians enslave humanity.