In the episode "The Conqueror", Zarm makes all the Planeteers, except forMa-Ti, fight with one another and nearly succeeds in having them destroy some nuclear missiles. What the four kids don't know for quite a long time, is that by obeying Zarm, they betrayed Gaia, who consequently became mortal (and apparently lost a great part of her powers). Seeing Ma-Ti cry of helplessness and hearing Gaia's almost resigned voice is heart-breaking. Thankfully, it's followed by a heartwarming part.
Or how about the "Two Futures" double episode, where Wheeler goes to an alternative future where he didn't join the team? He sees a dystopian world and the other Planeteers living different lives such as Ma Ti as a beggar who uses his power to get passerbys to give money to him. Probably even sadder is Wheeler going to Hope Island which is now a sleazy pleasure resort akin to Las Vegas or Atlantic City and finding Gaia's dead body surrounded by toxic waste.
In "Heat Wave", Gaia's life is in great danger, due to the greenhouse effect of Dr. Blight's force-field dome over Hope Island. When the Planeteers, after saving Linka and stopping the toxic fumes from being pumped under the dome, return to the island, they find Gaia dying. And yet, it's her who gives them a tip on how to call Captain Planet from inside the force-field.
In the episode "Mind Pollution", thanks to Verminous Skumm handing out drugs called "Bliss" to everyone, Linka's cousin Boris goes crazy, jumps out of the window of the second story of a building, survives his injuries and ODs on the whole bottle of Bliss that was given to him before he dies of a fatal overdose.
In the episode "The Great Tree Heist," Captain Planet is so badly wounded by Greedly that when the Planeteers try to bring him back, he can't manifest. The Planeteers think he's dead; the conversation that follows- unable to say "dead," denial and crying - is heartbreaking. Even worse is that 3 out of the 5 Planeteers are orphans and Captain Planet is implied to be their surrogate/adoptive father. NOW go watch the scene.
"A Formula For Hate" episode qualifies too. A young high school basketball player Todd Andrews finds out that he is HIV positive, this of course makes him concerned and depressed. Then Verminous Skumm uses this as means to take over the world: by lying by townspeople about AIDS and spreading lies about it. He becomes victim of bullies, his own best friend rejects him, he lies to his girlfriend to protect her and she thinks that he dumped her and later townspeople attack him, his mom and their living place and his little brother was beaten. In the end of episode, with the help from his coach, everyone accepts him and feel guilty about their treatment towards him and there is An Aesop that HIV positive people are need care and support, not scorn and harassment. However despite the fact that everyone accepted Todd, episode's ending is Bittersweet Ending at best, because Todd will not have a chance to marry his girlfriend and have kids because he'll infect his potential kids with HIV and Todd probably won't live very long if his HIV turns to full-blown AIDS (unless he spends a lot of time and a lot of money on getting it under control, but even that's not very likely).
The episode "Planeteers Under Glass" while in a simulation featuring different biodomes, simulating a few centuries in minutes. The Planeteers get trapped inside by Blight who changes everything into a hellish nightmare version of the earth. At one point a simulated animal saves Gi from drowning, and the pair become friends until they get separated. Sadly, as Blight continues to make things worse. The group runs into Gi's new friend, only for it to die moments later.
Wheeler's dream in "Numbers Game" has some comedic moments in how over-the-top it is, but think about it. Wheeler came from a broken home in which his abusive father constantly told him that he was a failure and a loser. In the dream, the friends he sees as family, including Gaia and Captain Planet, have stopped caring about him or anything else, making Wheeler's worst fear - everyone he loves turning away from him - horribly real. Still funny?
"Whoo Gives a Hoot?" The Planeteers attempt to stop Looten Plunder with a court injunction against clear-cutting an old growth forest where an endangered species of owl lives. They fail and the episode ends on that note, with Plunder taunting them to try and stop him again.
If you like animals, don't under any circumstances watch "101 mutations".