Responding to a gravitational disturbance in the Caelin system, the Primate Avenger is shot down and sinks to the bottom of the vast pink ocean covering the planet. But the monkeys don't drown for a very peculiar reason. Now these underwater monkeys must stop the two warring factions on the planet before they destroy their own world. That is, if they can survive a totally wild battle on surfboards, a sea quake and the molten lava racing for the downed Primate Avenger. Cow-a-monkey-bunga, dude!
What the Space Monkeys need are a few good androids to take over for them in defending the universe. But all Dr. Splitz can do is make a friend for Gor out of twine and paper clips: a cute little orangutan android named Isaac. When the crew goes in search of more advanced machines on Cyber 1, the monkeys discover the planet is run by the former computer, Matrix, who believes he has created life -- a whole civilization of robots. Will the monkeys escape this cybernetic nightmare... and is Isaac more monkey or machine??
The Space Monkeys take a "shortcut" through a wormhole and get caught in a sub-space speed trap. The Primate Avenger is towed to an asteroid where the monkeys stand trial -- all except Shao Lin, who refuses to leave the ship. It's a good thing too, because the judge turns out to be none other than Apax, the intergalactic con-artist, who throws them into prison where deadly Rolpenoids stand guard. Now it's up to Shao Lin to break her friends out of jail and bring Apax to real justice.
The Space Monkeys land on a planet where humans are primitive and warlike (imagine the chances of that!) and two stranded alien creatures are undergoing a rite of passage. While one of the young aliens, Larnus, befriends the monkeys, his brother, Tronus, joins with the humans to capture them. As the monkeys seem outnumbered, the adult aliens arrive to pass judgment on their young and reveal a world where evolution doesn't quite work the way you might expect.
Running from a space shark and nearly out of fuel, the Space Monkeys ride a meteor through a wormhole. On the other side, they discover that the meteor is about to hit a planet. They try to warn the alien-wary inhabitants, but the universal translator is broken! Despite repeated attempts to communicate, they cannot convince the inhabitants of their peaceful intentions. So, to save the paranoid planet...they invade! It's the attack of the Alien Space Monkeys!
Rhesus 2 tricks the crew into replacing their Holo-boon generator with one he can control. The new Holo-boons, led by the evil Holo-boon 3462/83B, organize a fascist takeover of the ship. The prancing 3462/83B proves disloyal even to Rhesus 2 and seems invincible. It all comes down to the Captain's desperate plan, involving timing, precision, cunning and Muzak!
While trying to stop Rhesus 2 from stealing gravitons from a cosmic storm, Simian gets a glimpse into another universe, where he encounters Vog, a one-dimensional alien. Back on the ship, everyone thinks Simian has gone coconuts when he claims to keep seeing the invisible alien. As Rhesus 2 attacks, Shao Lin must decide whether Simian is capable of commanding the ship.