The Planeteers argue about their priorities concerning different ecological problems. Sly Sludge dumps waste in a salt mine. Gaia assigns the Planeteers to intervene so they can end the dispute between themselves.
Linka leaves the Planeteers and returns home to look after her sick grandmother. Something is poisoning the water and the Planeteers begin to investigate. After they discover the culprit, Linka rejoins her friends.
Dr. Blight succeeds in constructing a machine, which switches the minds of two affected bodies. She manages to take over Gaia's body and Gaia herself inhabits Dr. Blight's body.
The Planeteers struggle to return endangered species to their habitats as they are being destroyed by the eco-villains. They end up rescuing far more animals than returning, to Gaia's dismay.
Gi visits a dolphin research center. Hoggish Greedly is behind a number of dolphins getting hurt due to his use of them to collect toxic waste from a submarine.
Zarm travels to the future and summons the great-great-great-grandchildren of 3 eco-villains. Captain Planet and the Planeteers can't handle the futuristic villains. Captain Planet is trapped and melted into a toxic acid bubble.
Wheeler's father is ill. Although they were never close, Wheeler heads back to New York. There he meets his old friends. Wheeler discovers that his friend Trish became Trash and turn to crime under Verminous Scum's orders.
The Planeteers go undercover to investigate a series of explosions at a plant. It turns Hoggish Greedly is behind the explosions, and the Planeteers call Captain Planet, who captures Greedly.
The Planeteers investigate the movie producer Robin Plunder who is the nephew of Looten Plunder. Meanwhile bats are being framed for terrorizing people.
The Planeteers are baffled when Hoggish Greedley gets a permit from an Army Corp of Engineers official to build houses by wetlands. Greedley has them and Captain Planet arrested and thrown in jail.
Looten Plunder devices a plan to ruin an environmental sustainable ranching operation. Captain Planet defeats Plunder, who is hauled off to jail-again.
The Planeteers participate in Dr. Derek's latest experiment on the long term effects of pollution on the ecological system. In the midst of the experiment, Dr. Blight shows up ad traps them inside the simulated computer world. Now it's a race against nature and time to save their own lives.
A teacher, who is an old friend of Gi is caught up in a gang war and nearly killed. The Planeteers infiltrate the two feuding gangs and try to stop all of the violence.
