Professor Farnsworth finds out that his clone Cubert was unable to go to school due to the large mob of Creationist protesters outside. Outraged, he quickly takes the Planet Express Ship to Wozniak Nerd Academy, where he finds himself arguing against anti-evolution protesters, led by Dr. Banjo, a hyper-intelligent orangutan who believes in "Creaturism," a form of creationism. In an attempt to prove evolution did occur, the Professor excavates the lost missing link, which he dubs Homo farnsworth. At the Professor's presentation of his findings at the Museum of Natural History, Dr. Banjo depicts Homo farnsworth anachronistically riding a Stegosaurus in an attempt to support his Creaturist beliefs. The Professor becomes fed up and resolves to leave Earth. He takes the rest of the crew with him to an abandoned planet to live in solitude, but leaves Cubert in the care of his godfather, Dr. Zoidberg, back on Earth. During this time, Dr. Zoidberg tries unsuccessfully to win Cubert's affection.
After the crew helps the Professor set up his home on the new planet, he inserts nanobots into the nearby pond to clean the water. However, in rapid time, the nanobots group into larger organisms, forming into trilobots that devour the ship and everything else. The crew is stranded and flee inside a cave. The next day, the crew goes outside and sees a newly grown mechanical forest. The nanobots have continued to evolve rapidly into flora and fauna. Robotic versions of Elasmosaurus and Tyrannosaurus rex attack the crew, but a robotic Triceratops (dubbed "Tricycle-tops" by the professor) saves the crew. A robotic Pteranodon 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, but a solar flare short circuits the dinosaur robots, causing a mass extinction of every robot creature except for "small mammalian robots" that were hiding in caves, including Bender. Within two hours, using the remains of the dinosaurs, the Professor manages to build a solar powered working space ship to help them return to Earth.
The next day, the crew wakes up to find both Leela and Amy kidnapped by caveman-like robots. The Professor makes a slingshot to fight the robot caveman. It takes him twelve hours to make the slingshot. They find that Leela and Amy are free, because the robot cavemen have since evolved into a completely civilized, modern robot society. They encounter a robot naturalist named Dr. Widnar, who is astounded to find her theories on organic creature evolution proven, and presents the crew at the Museum of Natural Robo-History. While giving a speech to the crowd of robots, the Professor states that he is proud of the nanobots' growth after he dumped their ancestors in a pond a few days ago. The robots, who believe unquestioningly in robot evolution, are angered by Farnsworth, and a Robo-Farnsworth states that 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. As proof, he shows a picture of a robot (Bender) riding a robot Stegosaurus at the start of their creation. Just as Dr. Widnar resolves to leave her planet similar to what the Professor said, the angry robots then arrest Farnsworth and put him on trial for "crimes against science". Bender represents him in court and in his arguments, states that the Professor is not arguing against evolution, but only claims a small role in beginning it by providing the materials necessary (the nanobots). The jurors leave to deliberate overnight.
The crew wakes up to find that the robots have now evolved into a state of incorporeal transcendent higher consciousness. They are no longer concerned with the Professor any more, finding corporeal beings altogether irrelevant. The crew then takes their makeshift spaceship home. There, the Professor explains his findings to Dr. Banjo. The Professor and Dr. Banjo reconcile their differences, acknowledging that both theories have some plausibility and even some correlation. Dr. Banjo argues that what the Professor witnessed was evolution, however evolution set in motion by an intelligent creator. The Professor agrees that it is possible, however unlikely that Earth evolution was set in motion the same way. However, they quickly prove to have not learned the lesson of tolerating others' views and beliefs, laughing off Bender's theory that this "creator" entity may be a robot, saying "And who created that robot? Some magic bearded robot in the sky?" despite having already proved his point in the episode (and this last is supported by the fact that Bender met God in person).
- Ascended to a Higher Plane of Existence: The crew are saved from being accused of creationism by the jury, the judge and indeed every robot on the planet evolving into energy beings overnight, and deciding their petty squabbles don't matter.
- Artistic License Paleontology:
- Invoked. Dr. Banjo unveils a (highly-inaccurate) mural of Homo farnsworth "frolicking with dinosaurs at the moment of creation".
- Played straight when they imply that Darwinius masilae was descended from apes, and its illustration shown on the holographic evolutionary chain doesn't resemble the real thing and instead looks more like a generic ape. (The real creature was an ape ancestor that looked a bit like a primitive lemur.)
- Clothing Damage: The nanobots, after becoming trilobots, devour the ship, Farnsworth's new house... and most of the crew's clothes.
- Continuity Nod:
- Finding a fossilized dog, Hermes assumes it belongs to Fry, like Seymour, and destroys it before Fry can notice.
- The solar flare causes Fry's hair to turn into a Fry-fro again.
- Even Bad Men Love Their Mamas: Brett Blob almost beats up Cubert for dissing his mom.
- Everyone Has Standards: Fry loves pineapples, but even he won't eat it on pizza.
- Everything's Better with Dinosaurs: The robo-dinosaurs.
- Fingore: When the Planet Express Crew is digging for fossils, Amy accidentally chisels off one of her fingers. It ends up in Fry's soup.
- Hollywood Evolution:
- According to Bender, the nanobots evolved so quickly because robots are so much more efficient than living things.
- Leela finds a missing link that's half-man, half-Toucan.
- Inadvertent Entrance Cue: Witnessing the solar flare, the Professor says only puny, mammal-like robots cowering in caves would have survived it. Bender then emerges from the cave they'd been sleeping in, oblivious to what's just happened.
- I Resemble That Remark!: When the Professor tells the protesters to "get on your turnip trucks and go home", it cuts to the Moon Farmer standing by a truck filled with turnips, who grumbles about the insultingly accurate stereotype.
- Ironic Echo: "I don't want to live on this planet anymore." Said first by the Professor and then later by Dr. Widnar.
- Kick the Dog: The episode ends with Zoidberg telling everyone that, after a subplot about the two bonding, he hates Cubert. Remember, this is Zoidberg we're talking about.
- Moving the Goalposts: Dr. Banjo does this on the Professor at Wozniak Nerd Academy, latching onto the absense of a missing link between apes and Darwinius masilae as proof that life was intelligently designed (basically a Creaturist equivalent to God of the Gaps) while dismissing the literal dozens of missing links Farnsworth presented.
- Ptero Soarer: The robot Pteranodon that carries off Fry to feed to its young.
- Running Gag: Bender insisting robots on Earth are the product of evolution, rather than research and development.
- Screw This, I'm Outta Here!: The afore mentioned "I don't want to live on this planet anymore." when said by the Professor. Then by his robotic equivalent.
- The episode's title is a reference to A Clockwork Orange.
- On display in the robot natural history museum is, among others, R2-D2.
- Skewed Priorities: The Planet Express crew has plenty of food to eat when stranded on the planet... but it's pineapple pizza, so they don't want to touch it.
- Stock Dinosaurs: Robotic versions of trilobites, Elasmosaurus, Tyrannosaurus rex, Triceratops, Pteranodon, Dimetrodon, Stegosaurus, and Smilodon (as a museum display) appear in the episode.
- Take That!:
Protester Parent: I don't understand evolution and I have to protect my kids from understanding it! We will not give in to the thinkers!
- The episode's Central Theme is based around the argument of Evolution vs. Creationism. While Evolution is untouched (before the Mechanical Lifeforms start evolving, anyway), the episode's stand-in for Creationism - Creaturism - is portrayed as blatantly pseudo-intellectualist. Dr. Banjo, a scientific professional that believes in Creaturism, consistently Moves the the Goalposts when it comes to the many missing links between man and ape and either latches onto an absence of evidence or uses non-permissable evidence (like a commissioned mural of Homo Farnsworth with a dinosaur that he likely commissioned himself) to prove his own point.
- Fry's initial analysis of the pool of minerals is that it looks like Dr. Pepper. Professor Farnsworth assures him it's "not that bad"... just toxic. Then, everyone refuses to eat pineapple pizza, even when there's no other alternative.
- The Triple: In his vein of missing links, the Professor finds "Java Man, Piltdown Man and Manfred Mann".
- To The Thememobile: The Science Mobile... by which the Professor just means the Planet Express Ship.
- Tyrannosaurus rex: Naturally, the first robo-dinosaur the crew encounters is a robot T. rex
- Wounded Gazelle Gambit: Zoidberg earns Cubert's respect by teaching him to do this when dealing with bullies.