At Springfield Elementary School, Principal Skinner is showing Mrs. Krabappel's class a time capsule that they intend to open a thousand years later and tells the students to each put something inside of the capsule. Bart, having forgotten to bring something to put in it, puts a sandwich that he blows his nose on into it. At a ceremony, Mayor Quimby lowers the time capsule into the town square in front of the statue of Jebediah Springfield. When they dig up the hole, they notice some green ooze pouring out.
Later that night, the Simpsons hear a strange noise outside like something falling from the sky. Marge then hears something glugging and belching downstairs. Homer and Bart decide to go to the basement and investigate. Down in the basement, Bart sees a shadowy figure opening up a can of Duff Beer, who is revealed to be Bender, who reveals he is from the future. Homer and Bender become instant best friends. The next day, Lisa starts to doubt that Bender is actually from the future, since robotic technology in the present is relatively advanced, so Lisa takes Bender to Professor Frink's laboratory. Bender admits that he does not recall why he was sent to the present, so Frink unplugs and replugs Bender's mission protocol, causing Bender to reveal his mission is to terminate Homer; however, he cannot do it, having developed a close friendship with him. A hologram of Turanga Leela and Philip J. Fry and some rabbit-shaped creatures that are attacking New New York appears. Seeing that Bender has not yet killed Homer, Leela and Fry encourage Bender to kill Homer. Lisa asks why he must be killed, and Professor Hubert Farnsworth replies that the creatures have Homer's DNA and Bender was sent back to kill Homer before the creatures could evolve from him. The Professor, Leela and Fry go into the past to kill Homer themselves, but Bender protects Homer, preventing Leela from shooting him. Everyone goes home but Farnsworth, Frink and Lisa, who stay back at the lab to analyse a DNA sample.
Farnsworth, Frink and Lisa get to the house; the Professor reveals that the DNA was only half of Homer's, with the other half belonging to Marge; they must kill one of their children instead now. Bender's rear shows a hologram of the creatures attacking Linda and Morbo, who report that the creatures have started evolving. One of the rabbits eats Linda and transforms into a lizard-like creature that resembles Bart. Bart remembers that when he put his sandwich in the time capsule, it touched Milhouse's lucky rabbit's foot and the toxic ooze in the hole touched the items in the time capsule mutating them into rabbit-like creatures with Bart's DNA. The Simpsons and the Planet Express crew arrive in the town square to dig up the capsule, but the portal the crew travelled through is damaged, and all of the Simpsons and the crew but Maggie and Bender are sent to the year 3014.
The Simpsons all hang out at the Planet Express headquarters, having failed to figure out a way to stop the creatures. However, Lisa is surprised everyone has given up. The Professor then proposes they shoot all the creatures into space. Lisa helps lure the creatures into Madison Cube Garden; the Planet Express Ship lifts the cube up and hurls it into space.
Back in the present, Bender takes Maggie to the race tracks, having known every result and winning a large sum of money. They successfully fix the portal and the Simpson family re-arrive back in the present. Bender then sets an alarm for 1,000 years and goes to sleep. Homer throws him in the basement but not before giving him a beer, which Bender appreciates.
The creatures are revealed to have landed on Omicron Persei 8, in which Kang and Kodos visit, who reveal that they are a same-sex couple.