On vacation, Linka goes to Washington D.C. to visit her cousin and uncle. Unfortunately, trouble isn't too far behind, because Verminous Skumm has brainwashed her cousin into taking a new drug called Bliss, and now Skumm wants to have Linka under his power as well.

To make a fast buck from a trash strike, Sly Sludge steals an untested microbe from Gi's scientist hero, Dr. Helix. It was supposed to be a technological fix for the problem of overflowing landfills, but it simply absorbs trash to become a city-devouring garbage blob. The blob must be stopped before it grows out of control.

Ma-ti is fooled when Looten Plunder disguises himself as a scientist, promising to clear the air all over the world, including his tribe's village in the rainforest. After Wheeler and the tribe are trapped inside one of Plunder's domes, and Ma-ti is captured after discovering Plunder's scheme, the remaining Planeteers have to find them both and bring Plunder down.

On the island of Mogahl, Looten Plunder and Dr. Blight have teamed up, and Blight's new cloning device will be used to clone workers for Plunder's flamethrower factory. They test it on the first living subject they find - a locust. But before they can capture the other one to test for side effects, it gets away. While searching for it, they come across Vico, a boy of a local village. He becomes the source for cloning workers for the factory. He becomes out of control with cloning when his appetite goes on a rampage, and threatens to wipe out the island. Now, the Planeteers (with the help of Captain Planet) must reverse the effects of the cloning ray, and also stop the locust(s) that have been cloned.

In the Florida Keys, Ma-Ti has a brush with what he thinks is a giant man eating shark, though Gi reveals that it is a harmless Basking Shark. When a local overhears and misinterprets their conversation, panic spreads throughout the resort town, whose mayor then hires Argos Bleak to eradicate all the sharks in the bay. Then, when stinging jellyfish (that the sharks used to feed on) swarm the beach, the townspeople learn that predators have an important role in the ecosystem. After escaping their sinking EcoCopter that was shot down by Bleak, the other Planeteers rescue Gi and Ma-Ti (who were captured earlier by Bleak) . . . and the Basking Shark . . . from bloodthirsty Bleak.

An alien (named Collectore) with good intentions abducts the Planeteers, convinced that the Planet Earth is doomed and decides to collect human specimens and include them in his menegerie of assorted alien life forms. The Planeteers must convince the Alien that Earth can be saved before Dr. Blight and Hoggish Greedly can destroy a forest, permanently eliminating the tiger population....

The Planeteers are saved from crashing by a solar beam, created by Dr. Pollo. He and his daughter live on an island, creating new and innovative ways to use solar power. Kwame falls in love with his daughter, while also becoming suspicious of their lab assistant, who turns out to be Leadsuit, sidekick to Duke Nukem. Nukem's plan is to turn their solar convertor box into a nuclear device, so he can feed on the nuclear energy generated by the beam that saved the Planeteers earlier. The Planeteers and Captain Planet stop Nukem in his tracks, but shocks from the nuclear energy erases Dr. Pollo's memory, prompting him to set out to rediscover his inventions.

A fishing village is taught a lesson about the coral reef when Hoggish Greedly shows up. He uses dynamite fishing as a cover to rip off the coral reef remains with his new Reef Ripper. The villagers don't see this, as they are now being well fed by a plentiful, but quickly disappearing fish supply. When shown the devastating effects of pounding waves against a neighboring island village, the villagers ask the Planeteers to help stop Greedly. Captain Planet finds a creative way to recycle, and help start a new reef....

People are collapsing in San Francisco with symptoms that suggest a whole range of pollution poisoning. As the Planeteers follow clues to solve this mystery, Ma-Ti (who is reading 1940s detective novels) keeps imagining himself as a private eye in black-and-white sequences. Ma-Ti proves a poor sleuth at first, but eventually he tracks down Verminous Skumm who is serving seafood tainted by storm drain runoff in his restaurant, The Sinking Ship.

Sludge and four of the Planeteers learn first hand the terrible effects of untreated sewage when MAL and Dr. Blight shrink the EcoSub (and them) to microscopic size and put them into polluted water that Kwame unwittingly drinks. The Planeteers must battle hideous water-borne parasites in Kwame's body so that he can recover, and restore them to proper size.

While the Planeteers learn about organic farming, Plunder exploits Joe, a man who cannot read, by tricking him into signing a contract allowing the distribution of pesticides on a farm that he manages.

Pete, a dirt bike enthusiast, tags along with Hoggish Greedly and Rigger, until Ma-Ti and desert guide Joshua Stone show him how alive the "barren" desert really is. They must get ahead of Greedly's ORV race to save the desert from being destroyed.

The Planeteers are present for the testing of JASON, a robot that observes wildlife and the environment, and transmits the data to its home base. The tests are being done on the Galapagos Islands, which is where Hoggish Greedly, Verminous Skumm and his rats have crash landed, since their ship was thrown off course from a storm. Now, they're hungry, and consider feasting on tortoise eggs to fill their appetites. The Planeteers must fly to the Galapagos to save the eggs, and remove the rats from the environment to restore the balance of its ecosystem.

Gi and Linka are livid when Wheeler belittles their favorite rock singer, but it looks as though Wheeler may be right after they come upon a land-ravaging, strip-mining operation run by Hoggish Greedly, but bankrolled by none other than their idol - Sky Runner! Stunned, they confront the star, who turns out to be innocent, but they still have to stop Greedly before the small mining town is destroyed.

When air pollution suddenly skyrockets in an Australian city with one of the best mass transit systems in the world, Gaia is suspicious. The Planeteers investigate and find out Looten Plunder and Argos Bleak are behind the problem. They are making it look like the transit line is haunted so that they can profit from massive freeway system and auto-related businesses. Thanks to teamwork Captain Planet and the Planeteers get things "back on track"

Linka and Ma-Ti visit a friend, Juan, in Central America. While there, Juan's parrot, El Profesor, leads them to a secluded "bird paradise" when suddenly, a giant, metallic bird appears. All the birds, including El Profesor, follow it and so do Linka and Ma-Ti. They soon find themselves locked in a huge aviary, courtesy of Hoggish Greedly, who's running an exotic bird smuggling venture. El Profesor escapes and leads the Planeteers back to the aviary, where they summon Captain Planet, who closes down Greedly's "fly-by-night" operation.

As key World leaders come together under one roof to discuss how to best prevent the growing spread of pollution and o-zone damage worldwide, Zarm returns to earth with a plot to snuff out the Planeteers. Calling a meeting of all the eco-warriors greatest foes, Zarm is able to tap into earth's energies and drain the earth itself of all it's resources. Only Gaia stands in his way, but Zarm has a final surprise to ensure she does not become a problem..

Zarm, having disabled Gaia and re-taken his position as spirit of the earth, begins turning the world into little more than a dead husk. With Gaia reduced to an old woman with not much longer to live, the Planeteers and Captain Planet face their greatest threat yet...

The Planeteers return to Kwame's homeland, Africa, to investigate strange happenings with cattle that was reported by his long-time friend and brother figure, Dr. Mabutu. Little do they know, Dr. Blight is there, scheming to convince a tribe leader (also a friend of Mabutu) to allow the injection of a serum that turns bulls into super steers in order to resolve their meat supply woes. Not only does this threaten the condition of the land, via excessive grazing, but the serum causes awkward side effects, which eventually does wear off. The Planeteers, with a hand from Captain Planet, manage to rid the land of Blight and MAL.

During an earthquake, a blow to his head leaves Wheeler lost from the others and suffering from amnesia. He finds himself literally in the shoes of a homeless man, and learns that the only difference between them is a simple twist of fate. A bang to the head restores Wheeler's memory, and he helps summon Captain Planet to rescue Teresa from a slum fire. Teresa and some shantytown residents decide to return to the countryside to pool their skills and make life better there.

The Planeteers travel to the Northwest after hearing about an old growth forest which is, literally, disappearing into thin air. After Wheeler goes off to investigate with a pretty local teenage bird watcher, Linka spots a "flying saucer" but Kwame recognizes the pilot . . . Hoggish Greedly! They discover Greedly's scam - "Sucking up" 500-year-old trees to make pressed board furniture. Outraged, they try to stop him, but his "Tree Trasher" may be too much for them.

A roofless dictator decimates the land to fight the opposition, with total disregard to the environment and human life. But there is more to the story than meets the eye. The dictator is really an old foe of the Planeteers in disguise.

Venice's population is relocating due to its pollution and smog affecting the land and structures - but also because of a large mutated group of rats whose bites sicken their victims. The Planeteers arrive and meet a pathologist, Resa, attempting to find a cure for the disease they cause that her young relative Pietre is suffering, and learn through clues that Verminous Skumm is behind it. But it isn't until Ma-Ti is bitten, and badly suffers, that they learn that Skumm is doing it through a substance placed in processed cheese that causes the rats and whoever they attack to become infected by contaminated canal-water. Now they have to find a cure for the worsening patients and stop the rats from terrorizing the populace with the contamination they thrive on.

Sly Sludge and Duke Nukem dump toxic waste in the Amazon rain forest, imperiling Ma-Ti's village. Ma-Ti returns to the village with Planeteers and find it in flames. When they fail to stop the fire, Ma-Ti hunts the culprits alone.

The Planeteers are shocked to see a mother whale killed during a whaling expedition engineered by Blight and Plunder. They are even more shocked to learn that it's legal, thanks to a loophole in the international laws that allow whaling for "research." They set out to prove that Blight's research for a "whale repellent" is bogus and are helped by a young Japanese teenager who is trying to dissuade his whaler father from working for the villains.