Chuck, Sue and Sandy's plane has been forced down on Mystery Island by the evil Dr. Strange, who needs their robot P.O.P.S. to complete his plan for world domination. After a frightening encounter with the mysterious Mud People, P.O.P.S. activates his force field to protect the group, but not in time to prevent Krieg and his henchmen from targeting Chuck with Dr. Strange's Gravity Ray gun.
After successfully repelling Krieg and his men using P.O.P.S.'s force field, Sandy finds Chuck immobilized by the Gravity Ray gun with a tiger about to attack him. After P.O.P.S. uses his gift of animal mimicry to send the tiger away, he frees Chuck by again using his force field. Immediately afterwards, they realize that Sue is missing – she has been captured and taken to Dr. Strange's cave, where she is fighting an intense battle of wills with the mad scientist's Mind Interrogator machine.
As Sue struggles to keep from revealing the secret of P.O.P.S.'s circuitry, Chuck and Sandy anxiously search for her. While scouting ahead, Sandy falls into a trap set by the Mud People, but Chuck and P.O.P.S. come to his rescue. Chuck and Sandy afterwards find the hidden cave, sneak past the henchmen, outwit Dr. Strange and escape with Sue – but then discover that P.O.P.S. is gone!
Chuck, Sue and Sandy follow Krieg and his men to the Valley of Fire, having overheard Dr. Strange order them to go there to track down their robot, taken by the Mud People in their mistaken belief he is a god. The trio get distracted by the Lava Man, a giant living creature miraculously formed from molten rock, trapped under a boulder from which they free him at Sue's insistence. The Lava Man appears to be grateful especially to Sue, and he moves on. Afterwards, the trio catch up to P.O.P.S. who has been abandoned by the Mud People in the Valley, only to be endangered by a huge volcanic explosion.
P.O.P.S. is rescued by the unlikely trio of Chuck, Krieg and the leader of the Mud People following another huge explosion in the Valley of Fire, while Krieg's men guide Sue and Sandy to safer ground. After everyone is safely out of the Valley, the Lava Man frightens off Krieg and his thugs to repay P.O.P.S.' human friends for saving his life earlier, but once he leaves again, the Mud People return to reclaim P.O.P.S. as their "god."
Chuck, Sue, Sandy and P.O.P.S. are brought by the Mud People into their cave where they encounter the Sentinels of Time – small, white glowing firefly-like creatures which can freeze people in time. Chuck and Sandy are suspended in time by the Sentinels who then chase Sue deeper into the cave, where she succeeds in repelling them upon discovering they can't stand her anti-deodorant spray. Her triumph is short-lived when she finds Chuck and Sandy have been unfrozen only to have the Mudmen expose them all to a mysterious mist putting them to sleep, not to awake for ten centuries, and P.O.P.S. is unable to help them, his battery running down from no access to solar power.
Dr. Strange discovers what has happened to P.O.P.S. and his friends, and through one of his inventions, tries to transport them out of their bodies to his cave. The process fails due to a sudden short circuit, but the exposure to solar energy rejuvenates P.O.P.S., enabling him to free Chuck, Sue, and Sandy from their sleep spell just in time for them to save him from being crushed by falling rocks. However, the whole process has some side effects, including the accidental transportation of mysterious beings from another dimension over to the island and, as the trio and their robot escape the cave, Chuck somehow undergoing a body switch with Krieg.
In Chuck's body, Krieg finally captures P.O.P.S. But with another short circuit, Chuck again becomes himself and then flees with the robot along with former captives Sue and Sandy on a raft, unaware they are heading for a waterfall.
When they realize their peril, Chuck, Sue and Sandy desperately try to save themselves from the waterfall as well as prevent water from seeping into P.O.P.S.'s circuits. Sue rewires the Gravity Ray Gun which they appropriated earlier, using it to push the raft toward shore. But immediately after they are out of danger, Sue suddenly vanishes – captured by a giant birdman.
Trapped in Black Cavern deep beneath Mystery Island, Sue is being slowly transformed into a birdwoman to be both princess and oracle for the Birdmen of Falconia, the aliens Dr. Strange accidentally transported to the island earlier. Meanwhile, Chuck separates from Sandy and P.O.P.S. during their search for Sue, leading to the latter two getting recaptured by Krieg and his men who bring them to Dr. Strange's cave. As Dr. Strange subjects P.O.P.S. to his own computer Titan, the energy process interrupts the Bird People's transformation of Sue. This leads the aliens to invade Dr. Strange's cave, turning off all power on Titan and placing everyone under their spell except for Chuck, who is outside the cave trying to find a way in.
Guided by messages from P.O.P.S, Chuck enters the secret cavern and challenges Wark, the leader of the Birdmen, to a duel of minds for the freedom and lives of himself and the others. Under P.O.P.S.'s guidance, Chuck wins and in grudging admiration, Wark frees everyone and goes with his people to seek for their oracle elsewhere. Once again surrounded by the thugs, Sue implores Dr. Strange, who does owe Chuck, to allow the group a 10-minute start to freedom; but he reneges upon discovering they are heading for the Kingdom of the Beasts.
Ignoring Dr. Strange's warning, the friends enter the Kingdom of the Beasts where Sandy, while scouting ahead, again falls into trouble, this time a bed of quicksand from which he is rescued by Sue while Chuck and P.O.P.S. use the robot's force field to repel yet another attack by Krieg and his men. The group soon discover a helicopter hidden by Dr. Strange in the jungle, but before they can get into it they are attacked by a lion.
After repelling the lion attack with the help of P.O.P.'s gift of animal mimicry, the trio decide to transfer the robot's computer brain from his body into a box, as they are unable to load him into the helicopter. They barely manage to escape recapture by Krieg and his men before taking off in the helicopter to -- they hope -- their freedom.
Dr. Strange sends a projector beam ray forcing the helicopter down, but Chuck manages to land it safely. Shortly afterwards however, the box with P.O.P.S.'s computer mind is stolen by a group of super-intelligent apes bred by Dr. Strange, led by the most intelligent of them, Korba. The Apes don't get far though before they encounter the Mud People who frighten them into dropping the box, which is then retrieved by Chuck, Sue and Sandy. Although they successfully reunite P.O.P.S. with his body, they are all still in danger.
The group seeks temporary shelter in a tree house, unaware Dr. Strange has it under surveillance, and soon find themselves besieged by the Apes. Upon learning from P.O.P.S. that the Apes are afraid of the Mud People, Chuck and Sue disguise Sandy as a Mudman, frightening their attackers away, but then they find their refuge is apparently caught in an earthquake -- courtesy of Dr. Strange -- and then a ghostly voice orders them to leave.
Confronted by the angry ghost of a pirate ordering the group to leave, Sue tries to attack it believing it to be a fake, but it disappears leading her to find a map that seems to indicate the location of a boat at the other end of the island. Led by the map, they race into a tunnel, and then into a trap transporting them back to Dr. Strange's cave. Unexpectedly however, they turn the tables by overpowering the mad scientist and subjecting him to his own Mind Interrogator to learn the way to the boat. Running from Krieg, his henchmen, the Mud People, the ape army and all of Dr. Strange's superpowers, they reach the boat and -- hopefully -- freedom at last!