Following his underwater adventure in Ecoquest: The Search for Cetus, Adam Greene and his father travel to the South American Rainforest for the Ecology Emergency Network to develop sustainable products with some of the local tribes. As they approach their destination of Iquitos in Peru by plane, they notice blasting going on in the wilderness. Determined to investigate it later on, they are unaware of the damage the blast really caused: the seedling of Forest Heart, a unique and ancient tree, also known as "She From Whom Everything Begins", was destroyed. With Forest Heart approaching the end of her life and with her child destroyed, the heartbeat of the forest will cease if no other seedling is found. Desperate for help she invites a human to save the forest: Adam. With help of the tribe of Cove People, the forest creatures and the bat Paquita, Adam goes on a search for Cibola, the City of Gold. However danger lurks as the ruthless Slaughter, who destroys the forests and its inhabitants for money, learns about the city of gold, and chases Adam whom he believes holds the secret to immeasurable wealth.
The Secret of the Rainforest, commonly referred to as "Ecoquest 2", was designed by Gano Haine, who also designed Ecoquest 1 (along with Jane Jensen). The game follows the same concept as its predecessor, teaching children about the fauna, flora and destruction of the rainforest, based on facts. It includes a recycle function, and contains a fact button that provides various elements of research. A new feature of Ecoquest 2 is the Ecorder, which allows Adam to record various things he encounters in the game - the player can also test his knowledge with the Ecorder to earn game points.
Although Ecoquest 1 was also released on Multimedia CD-ROM with voice actors, Ecoquest 2 was only released on floppy and only as a Sierra Discovery Series title, although there are a handful of spoken lines in the game. Sadly Ecoquest 2 was the last release of the Ecoquest series.