The crew answers a distress call from the NC-17 galaxy, where they find a derelict ship and split up to search it. Spydor uses his beamatron to pick up a pile of crystals. The crew then returns to their own ship, since they didn't find anyone alive, and also because Splitzy started a core meltdown. On their way out, Spydor uses the beamatron again to pick up an egg (which he thinks is a coconut).

Later, an alien hatches from the egg, attaches itself to Spydor's rear end, then escapes into the vents. The alien spits out radioactive mucus. By the time the crew finds it again, it has grown, and dodges their blasts. Splitzy says that the alien's DNA is changing rapidly, allowing it to change shape quickly; as Gor fights the alien, it absorbs his DNA, reconstructing itself and becoming stronger.

The ship is warped to a planet in another galaxy, where they are attacked by a missile (labeled "USA") and several unmanned planes. After blowing up the planes, they search the planet further, finding that it looks like Earth but is covered entirely with jungle, and meet an intelligent monkey named Lilith. Lilith identifies herself as the caretaker of the planet, and tells them that an alien race recently visited, got rid of all poverty and pollution, and made all species intelligent. The others all left to explore space, leaving her behind as the chosen caretaker. Captain Simian quickly falls for her, and she takes him to look around.

The rest of the crew continue to search the planet separately. Gor, Spydor, and Splitzy are attacked and captured by living vines. This turns out to be the work of Rhesus 2, who then confronts Captain Simian. Rhesus 2 explains that the planet isn't Earth, but his former homeworld Terrestria; long ago, its human scientists sent him into space, but his pod escaped orbit and was beamed on board by Lord Nebula, who made him intelligent. After their previous encounter, the immortal Nebula brought Rhesus 2 back to life and sent him searching for a substance called Uterium, which would allow Nebula to become a black hole once again. To this end, Rhesus 2 enslaved his homeworld; he attaches some of his brains to the crew, mind-controlling them so that they cannot escape, and adds them to the slave force.

The episode opens up with Gor having nightmares about crushing the ship. Shao Lin gives Gor a crystal necklace that she says will help him deal with his dreams. Later Splitzy intercepts a message between Lord Nebula and Rhesus 2, Nebula tells Rhesus 2 to go to a planet named Medusa 4, where he will find a device to produce the anti-force. Captain Charles Simian quickly gets to the planet. When they get there they are attacked by Rhesus 2 and his drone ships. the Primate Avenger gets damaged so the Space Monkeys hide behind an asteroid shield. Splitzy creates a holographic image of the ship and Rhesus 2's drone ships start attacking it and destroy each other in the process. Rhesus 2 then leaves the asteroid belt. The Monkey's think that he went back to Nebula for reinforcements, so they head to Medusa 4, to get the device for anti-force. The crew then starts searching the planet. Spydor falls down a trench and the rest follow after him. They land in a chamber, there they meet an alien named Grxylpk. Grxylpk takes them to a wall shaped like an ear, and tells them that this is the sacred ear. He adds that some say it was a sleeping giant around which the planet had crystallized. Grxylpk says that the sacred ear keeps the galaxy running and he whispers everything which gets printed from a computer and the ear makes them through his power of the dreams. None of the Monkeys except for Gor-illa believe Grxylpk. Then to prove Grxylpk wrong, Spydor tells the ear to create some bananas, and soon there is a pile of bananas in front of him.

The crew catches a coded message from Nasa, but the Monkeys couldn't translate it because the decoder was destroyed in the second episode. Later Splitzy finds that Charles' capsule was not destroyed with the planet and made its way to the XJ-12 galaxy. So the crew get ready to go there. When they get into the galaxy the Primate Avenger gets caught in a magnetic anomaly and crashes in a lifeless junkyard. So the crew goes searching the planet for something to fix their ship. Later a couple of robot attack the Monkeys. The Monkeys defeat the robots and later make their way to another robot that tells them that he is Matrix. The Matrix captures the Monkeys to "deconstruct and assimilate", and more robots arrive. Gor-illa gets free and then frees everyone else. However as the Monkeys are making their way to the ship, a robot captures Spydor and Gor.

On the ship Orbitron tells the Monkeys that 1,000 years ago, Matrix was an automated salvage vehicle that deconstructed and assimilated abandoned space vehicles. Later it was also caught in the anomaly and was trapped. Matrix then linked with other alien computers and continued de-constructing and assimilating. However the robot can't distinguish between machine and Monkeys.

The Primate Avenger is attacked by electric beams from an unknown ship. The ship keeps coming in and out of warp, so they can't track it. Later Splitzy finds out that they are scanning the ship for lifeforms with the electric beams. Later the ship beams up and kidnaps Gor and Spydor, and then the ship leaves. At the other ship Gor and Spydor are met by Apax, an alien who has snakes for hair. Apax tells Gor that he's going to make him a champion, and takes Gor and Spydor to an arena, where Gor is forced to fight. Meanwhile back on the Primate Avenger, Splitzy creates a device to capture the ship's warp trace, and then the Monkeys find the trace and head there. Back at the arena, Whenever he's put with a match with someone, Gor convinces them that fighting is wrong and talks them out of the ring. So then Apax tells Spydor that if Gor doesn't fight then he will kill him. So Spydor tells Gor to fight him, but Gor says he doesn't want to. Then Spydor tells Gor to pretend that his opponent eats caterpillars for breakfast, then Gor gets angry and starts fighting his opponent.

Gor had been having hard time keeping up with the rest of the crew, so Splitzy attempts to repair the cerebrotron to increase Gor's intelligence. When he tests it and it works, Gor's intelligence increases and he becomes smarter than Splitzy. Meanwhile Rhesus 2 finishes making his new invention, a robot named Lobiathan. Rhesus 2 then attacks a mining colony to get some anti-force for Nebula. The monkeys get a distress call and quickly go there. When they reach the colony Rhesus 2 attacks with his robot. The Monkeys couldn't stop Lobiathan, so they destroy the building that contained the anti-force. Then the Monkeys leave on the ship, but Rhesus 2 shoots a cannon and the ship crash lands. Then Rhesus 2 attacks the ship to get Gor's brain because Gor is now smart and knows how to create anti-force. Shao Lin and Charles attack Rhesus 2 in a fighter plane, but have no effect on the robot. Later Spydor tries to make Gor transform into Gormungus, so that he can defeat Rhesus 2. However, Gor has gotten too smart to get angry and Spydor's plan fails. Since Rhesus 2 wants Gor's brain because he is smart now, so Gor uses Splitzy's cerebrotron to decrease his intelligence back to how he was before. Then he transforms into Gormongus and destroys Rhesus 2's robot and defeats Rhesus 2.

Rhesus 2 destroys the Holo Boon generator to force the crew to Velasquez 9 for a replacement. Unbeknownst to them, he has modified the replacement to generate a megalomaniacal dictator whose "Holo Boon horde" seizes the ship.

The crew lands on an alien planet populated entirely by barbaric humans as well as two alien brothers who had been abandoned on the planet for three years as a test to enter adulthood. While one brother wandered alone the other allied himself with the human population who "knew how to survive." Unable to leave, the crew is captured by the human tribe which confirms many of their preconceived notions about humanity. Although Shao Lin was worshiped by humans on Earth and Simian claimed to have a good "working relationship" with them, Gor, Splitzy and Spydor had all been abused by various humans and Gor, who had been hunted by poachers back on Earth, especially disliked them. However, when Gor frightens a young human girl he finds her to be innocent and that humans are capable of change. When the brothers' father finally returns for his sons the crew rethinks what it means to be "evolved."

In a parody of Noir films, Captain Simian and the Space Monkeys must navigate the treacherous twists and turns of the denizens of Maltese 1 in order to recover the stolen Orbitron, which has revealed it contains the formula for GLOPP, before a local crimeboss can sell it to Lord Nebula.

The Primate Avenger comes across a spacecraft containing a huge forest of trees and plants. The roots of the trees suddenly come to life and drag the Avenger on board. The forest is dying and requires a gardener to maintain it. The nature-loving Gor would be ideal for the post and when his companions try to interfere their lives are put in jeopardy. To add to their problems, Splitzy unintentionally switches the minds of Simian and Shao Lin, resulting in them occupying each other's body.

A powerful being calling himself the Glyph offers Simian the chance of destroying Nebula. The plan is to lure Rhesus 2 into a trap and get him to lead them to his master. But the crew soon discovers that their new ally has an agenda of his own.

While the crew argues about whether or not they should try to return to Earth when the Universe is still in jeopardy Gor wishes he had a friend to share his interests. Splitzy has created a small android orangutan as an experiment and decides to use Gor's simple mind as a basis for its thought patterns. Gor names it Isaac and the Captain thinks an android crew might be the ideal solution to allow the Primate crew to go home. They travel to Cyber 1, an android planet, for parts to build their replacements although Shao Lin remains skeptical. When they arrive they find the planet is ruled by Matrix; a former enemy who attacks them and refuses to let them leave.

Meanwhile Gor and Splitzy argue about how Isaac should be, for want of a better term, parented. Their fighting causes Isaac to become confused about his identity and run away. When Isaac goes too far out on a ledge and falls, Gor and Splitzy risk their own safety to save him. Isaac does not understand altruism and Gor explains that "We are supposed to help each other." When they find the power grid for the planet, Issac decides to stay behind as he is the only one who can shut down the power grid to allow the others to escape. He declares that he is an android and belongs there, and says goodbye to Gor who he calls Father (and Splitzy who he calls 'Uncle'.) In light of Isaac's sacrifice and sense of duty, the Captain decides that the fight to save the universe is their responsibility and that they must continue on until it is completed.

Later Isaac is shown growing the planet's first organic flower and sharing it with the other androids.

Trivia: The theme from the movie Brazil is playing on Cyber 1. Brazil is set in a similarly dystopian world beset by advanced technology.