A psycho-neutron annihilator bomb destroys all life forms and can protect itself from being discovered. And Rhesus 2 has just put one on the Simian ship, forcing the monkeys to face their fears in order to disarm the bomb.
On a primitive planet, the Monkeys find two aliens undergoing a rite of passage. One alien befriends the monkeys, the other joins a group trying to capture the Monkeys. An intervention shows that things aren't what they seem.
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.
The Space Monkeys need a few androids to help in defending the universe. When the crew searches for more advanced machines on Cyber 1, they find the planet is run by Matrix, who believes he has created a whole civilization of robots.
In the Caelin system, the primate ship is shot down and sinks into the pink ocean covering the planet. But the monkeys don't drown and now find they must stop the two warring factions on the planet before they destroy it.
Nebula has the GLOP generator but needs one last part from the Primate Avenger. Attacked by the ganglia, the Space Monkeys are snared in Rhesus' energy net and about to be tortured. Will they be saved by their captain?
Capt Simian is lost on a world of illusion, and only a visit from the mysterious mandrill Mandrax can save him. Can he stop the madman Nebula from using the final component he needs to destroy the universe?