Dr. Zin bio-engineers an army of insects and disrupts the weather patterns of the Earth to become supreme emperor.
Jonny and Hadji run through the jungle from pursuers. They make it into a village and move to take a sapphire from a statue, but are surrounded by flames an guards. The flames fade and Chief Atacama steps forward. This was a test of manhood, but Jonny has failed due to lack of patience and caution.
In Earth's orbit, a satellite opens up. It fires on the Earth, causing violent weather disruption in the village where the Quest team is visiting. Quest gets an urgent call from Commander Harris at Intelligence One due to climactic anomalies.
The team returns to the Quest Headquarters in Mexico, where it's snowing. Jonny rushes in to work with 4-DAC. Dr. Quest and Race comment that Jonny is enthusiastic, but lacks patience or caution. The team analyzes the data. Jessie joins them. She suggests a major heat injection, and it appears to be occurring over the North pole. Dr. Quests contacts Quest Station in orbit, but Dr. Eve Belage tells them that their sensor abilities are nonoperational, so Dr. Quest and 4-DAC plan to take a replacement to the station.
Something crash-lands on Earth.
The birds are acting unusual, so Jonny, Hadji, and Jessie take off to investigate. They find the source of what scared the birds and other animals: armies of separate insects working together. Jonny crashes, but they rescue him and fly back to headquarters.
The kids report to Race and Dr. Quest. 4-DAC reports that the swarm is headed for Quest Headquarters. Dr. Quest asks why Jonny ran off on his own again, and Jonny said it because he wants to prove himself, but Dr. Quest encourages to him work with the team not around them, which needs patience. 4-DAC analyzes that there's a signal controlling the insects. Jonny brings up Chief Atacama's music that controls fireflies, and 4-DAC adapts the recording to redirect the insects.
Quest Shuttle 1 is ready for takeoff when the insects clog their exhaust and threaten the launch. They play chief Atacama's music, and free up the valves, and Dr. Quest and 4-DAC safely launch.
At a command center, 425 apologizes to Dr. Zin for failing to stop the launch. Dr. Zin can't have Dr. Quest discover his stealth satellites just yet. Dr. Zin has his insects carry off 425, and he promotes 426.
Quest Shuttle 1 docks with Quest Station and Dr. Eve Belage greets them. Aboard the station, Eve shows them the plant life and creatures that are flourishing on the station. 4-DAC gets Quest Station's sensors back online, and they connect with I-1 Central Command. 4-DAC begins to scan Zin's satellites, but they respond by unleashing a computer virus that infects 4-DAC, giving Zin's team complete control of it.
On the ground, Race and the kids are still looking into the situation with the insects. They encounter two large insects but destroy them.
Commander Harris contacts Dr. Quest with updates on the chaos the weather disruption is causing. 4-DAC goes to recharge its power packs, connecting directly into Quest Station and taking full control and accessing data to Dr. Zin. Zin gives further instruction to look into some of the research on the station.
Jessie looks parts of the insects, which appears to be partially synthetic. Jonny contacts 4-DAC to run a scan on the insect's appendage, but he finds that 4-DAC is offline. He reaches out to his father.
4-DAC, controlled by Zin, looks into a prehistoric insect in the genetic archives. He decides to bring Quest Station to him, and reveals his asteroid base as he takes control of Quest Station and prepares them to dock.
Everything is offline on Quest Station as they're docked to Zin's asteroid. Zin's army of insects surround the station. The insects invade Quest Station, and they would be driven back but 4-DAC intervenes on Zin's behalf. Zin greets Dr. Quest and Dr. Belage, and gives them a tour of his asteroid.
Meanwhile on the ground, they've lost all communication and tracking of Question Station. So Race and the kids prepare to go up in Quest Shuttle 2 to look for it. Commander Harris assists them, and they're able to launch through the poor weather.
Zin tells Dr. Quest and Dr. Belage about his insects, and about his plans to conquer the world. 4-DAC points out that storing so much ethanol is dangerous, and Zin has him dumped over the edge into ethanol.
The team aboard Quest Shuttle 2 continues searching, arriving at the Quest Station's last known location.
Dr. Zin begins creating a prehistoric insect, an assassinoid, from the genetic material aboard the Quest Station. His team spots the Quest Shuttle 2 getting closer, and they target it.
Zin is about to fire upon the Quest Shuttle 2. 426 stops him lest it reveals their position, but he sends her to her death and promotes 427.
Commander Harris tells Quest Shuttle 2 that they'll need to land before the weather prevents their return. They track 4-DAC instead of the station and are able to connect. They realize he's been infected with a virus, so they begin working on uninfecting him. Jonny is able to give 4-DAC back basic motor control, and he pulls himself out of the ethanol. He tells Jonny that Dr. Zin is behind the incident. Race reports back to Commander Harris.
Meanwhile, Dr. Belage and Dr. Quest try to talk Zin out of cloning a dangerous insect. Zin has them locked away and prepares his invasion force to take over Earth. 4-DAC, now under Jonny's control, breaks out Dr. Quest and Dr. Belage.
Quest Shuttle 2 encounters Zin's insects in space, and they're hit and Race is injured, and the shuttle begins falling to Earth.
The shuttle is damaged and Race is too hurt to pilot. Jonny and Jessie take control and are able to pull the shuttle back up from entering Earth's atmosphere.
Dr. Quest, Dr. Belage, and 4-DAC search for an escape. Dr. Zin blames 427 for the failure to stop Quest Shuttle 2 and prevent Dr. Quest and Dr. Belage from escaping, so he freezes him to death. He orders his insects to find Dr. Quest and Dr. Balage.
The kids are able to revive Race. Intelligence One reports that Dr. Zin must be cloaked like his satellites. Jonny is dejected, blaming himself for his mistakes. Jessie and Hadji encourage him and they begin working together again to find Zin.
Dr. Quest, Dr. Belage, and 4-DAC look for Dr. Zin's escape ship. 4-DAC distracts the insect guards for Dr. Quest and Dr. Balage can make it to the ship. 4-DAC is shot down in the process.
Jonny is no longer able to get a connection with 4-DAC, but they find another way to locate Dr. Zin's base. Intelligence One is unable to launch any support due to the weather conditions.
Zin recaptures Dr. Quest and Dr. Balage. His prehistoric insect clone army is almost ready. Dr. Zin contacts Commander Harris for their surrender.
The leaders of the world are ready to surrender to save their people.
The Quest team aboard the Quest Shuttle 2 finds an entry into the asteroid, but it will take work to get to it.
Dr. Zin attempts to drain all of Dr. Quest and Dr. Belage's knowledge into his computer to assist with his world domination. Alarms begin going off as the Quest Shuttle 2 approaches. Zin fires on the Quest Shuttle 2, destroying it.
The Quest team are safely aboard the Weasels and were piloting the shuttle remotely. They successfully enter Zin's asteroid undetected. They wear face masks to protect themselves from the ethanol. Jonny accesses Zin's computer, finding Quest Station, as well as his father on the other side of the station. They hold off releasing the virus into Zin's system to rescue Dr. Quest.
Dr. Zin's new insect Assassinoid emerges, and it attacks the other insects but it bonds with Zin. At another alarm, Zin sends the Assassinoid to find and destroy the infiltrators.
The insects catch up to the Quest Team, and Jonny and Jessie escape through a vent, but Race and Hadji are separated, pursued by the new insect Assassinoid. Bandit runs off, and Jonny and Jessie follow him to 4-DAC. Jonny pulls 4-DAC's CPU and plugs it into his Compuport. 4-DAC helps them find Dr. Quest. The insect catches up to them and the team reconvenes. They freeze the insect and it shatters. But after they leave, the shattered pieces reform into separate insects. The Quest team frees Quest Station.
On Earth, the world leaders have surrendered to Zin and the weather has stabilized. Intelligence Once receives a message from Quest Team.
The Quest team plans to freeze the piece of Assassinoid for now. Before they continue with their plan, Jessie gives Jonny a kiss on the cheek. As Jonny and Race run from the insects firing on them, Jonny falls and drops his Compuport.
Jonny gets his Compuport and brings out the Weasels to help them against the insects. Jonny and Race get through, and Hadji and Jessie lock into Quest Station. Jonny uploads the virus into Zin's computer system and takes control of the system. He allows for Quest Station to undock and escape Zin's asteroid. Race and Jonny make contact with Intelligence One to report on it.
Zin's computer upload of Dr. Quest and Dr. Belage fails and they're released. Race and Jonny arrive and save them.
Intelligence One has gained control of Zin's satellites and they turn them on Zin's asteroid to destroy it.
Alarms begin going off on the base. The team heads for Zin's escape capsules where they're met with Assassinoids. The Assassinoids shoot acid, which destroy one of the escape capsules. The Quest team escapes, and are helped by Jessie and Hadji in the Weasel. They escape the base on the Weasel, and Zin's base is destroyed in an explosion. They succeeded as a team.
Back on Earth with the tribe and Chief Atacama, Jonny and Hadji pass the test of adulthood. They invite Jessie into the circle to celebrate with them.
On the Quest Station, Dr. Eve Belage places the frozen Assassinoid in storage, suspending further research on it. The Quest Station continues its other, more beneficial growth research.
In space, a piece of Zin's asteroid is still intact.
- Dr. Zin
- 425 (only appearance; dies)
- 426 (only appearance; dies)
- 427 (only appearance; dies)
- Assassinoids (only appearance; dies)(no lines)
- South America
- North America
- I1 Central Command
- Quest Headquarters
- Europe (mentioned)
- Africa (mentioned)
- North Pole (mentioned)
- Quest Station
- Dr. Zin's astroid base
- 4-DAC is a reference to 3-DAC from the previous film.
- Jessie is riding the same type of hoverboard that Jonny rode in the previous film.
- Zin died in the previous film, with a clone surviving at the end. But whether this plot point was continued isn't clear, as it's not elaborated on. The Quest team never question why Zin is suddenly alive, perhaps because they're used to it.
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