A Clockwork Origin is a play on Anthony Burgess's 1962 dystopian novel A Clockwork Orange and the 1971 film adaptation by Stanley Kubrick with the same name. Like the novel and film, A Clockwork Origin spins a drama out of rival ideological claims about the nature of nature. In the novel and film human nature is at issue. Is human nature fixed or plastic? In the television episode all of nature is at issue. Is life the product of design or accident? The 'fixed' and 'design' positions are fundamentally conservative or rightist while the 'plastic' and 'accident' positions are fundamentally liberal or leftist.
After being interrupted by Cubert, Professor Farnsworth asks why he isn't at school. Cubert responds by saying that he couldn't get past the protesters. The Planet Express crew then sets out to Cubert's school where protesters are arguing against the teaching of the theory of evolution in schools. Farnsworth argues that evolution did occur, but is ignored because there is one missing link in history that has not been found (although every other link had been found to support evolution). Angered by the protesters' support of Creaturism (a form of creationism where an all powerful "creature" created life), the Professor decides to find the missing link and prove the theory of evolution. After searching for days, the crew eventually finds the missing link. Bender refuses to believe that Robots didn't evolve, but the rest of the crew ignores him, with the Professor stating that Robots were just recently built. The crew then presents the missing link (dubbed Homo Farnsworth) to a museum. Farnsworth is disgraced when an avid Creaturism supporter, Dr. Banjo, reveals a picture of Homo Farnsworth riding on a Dinosaur at the start of creation, stating that it disproves the theory of evolution. Farnsworth, disgraced and angry, decides that he doesn't want to live on Earth anymore.
After leaving Cubert with Dr. Zoidberg, the Planet Express crew sets out to help the Professor set up a house on a distant planet in deep space. After setting everything up, the Professor inserts nanobots into the nearby pond, to clean the irritants in the water. The nanobots then become larger, devouring the ship, Farnsworth's new house, and most of the crew's clothes. The crew hides in a cave, while Bender argues that this proves the theory of robot evolution. The next day, the crew goes outside and sees a newly grown mechanical forest. The nanobots have now become mechanical "dinosaurs". Robotic versions of Plesiosaurus and Tyrannosaurus Rex attack the crew, but a Tricycletops saves the crew. A robotic Pterodactyl takes Fry to her nest, where she is about to feed Fry to her robotic young. As the crew attempts to rescue Fry, they are ambushed by a robotic Dimetrodon and the same robotic Tyrannosaurus Rex, but a solar flare short circuits the robots (except for Bender who was not affected because he was hiding in the cave). The crew salvages the robot parts to build a spaceship, but they must wait until the next day because it is solar powered.
Meanwhile, Zoidberg tries to bond with Cubert, who admits that the reason he makes fun of people is because he's being bullied in school. Zoidberg, knowing full well that he himself had been bullied a whole lot in his childhood and then bullied a ton by his coworkers then gives Cubert advice on how to deal with bullies (by acting cowardly) and the two become closer.
The next day, the crew wakes up to find both Leela and Amy missing, taken and possibly raped by robot cavemen. They go outside and witness the cavemen carrying the women into a cave on top of a cliff. Bender explains that the fittest survived (survival of the fittest) and the Professor makes a slingshot to fight the robot caveman. It takes the professor 12 hours to make the slingshot, so everyone agrees to rescue the women the next day. When the guys wake up, they run out of the cave, ready to combat the caveman robots. Leela and Amy are standing outside the cave and explain that the robots (who wanted them as wives) disappeared after they had went to sleep. A "human like" naturalist robot comes out of the forest and attempts to capture the humans. After realizing that they can talk, she is very excited and so she takes them to the Museum of Natural Robo-History. There, the professor states that he's proud of the nanobots growth after he dumped their ancestors in a pond a few days ago. The robots (who believe in robot evolution) are angered by Farnsworth, and state their Earth took eons, not days, to be created. The professor explains that relative to them, it was eons, but in reality, only a few days had passed. He then shows a picture of a robot (Bender) riding a dinosaur at the start of their creation, thus disproving the theory of robot evolution. The angry robots then arrest Farnsworth for "crimes against science" and he is put on trial. Bender represents him and argues the Professor is not arguing against their evolution, but only claims a small role in applying the initial machinery. Bender calls this insanity and asks the jury to vote not guilty by means of insanity.
The jurors deliberate for so long that everyone falls asleep. When they wake up, the robots have evolved into a state of higher consciousness, and are not concerned with the Professor anymore. The crew then takes their makeshift spaceship and head home. There, the Professor explains his findings to Dr. Banjo. who agrees that what happened was some form of evolution, but it was set in motion by a wise and all knowing creator (Farnsworth). The Professor and Dr. Banjo then ridicule Bender for wondering if their creator was a robot, and Zoidberg admits he's happy to finally be rid of Cubert, who's "horrible." Everyone laughs and Zoidberg emphasizes his annoyance with Cubert.