Below the Root is based on Zilpha Keatley Snyder's fantasy book series "The Green-Sky Trilogy". Following the events in those books, The Kindar and the Erdling societies have joined together. However unrest and distrust still remains. An old woman, D'ol Falla has heard the words "The Spirit fades, in Darkness lying. A quest proclaim, the Light is dying". Choosing one of five available people (of different ages and of either Kindar or Erdling descent) either she believes can help, D'ol Falla assigns the quest of discovering what these words mean and how to quell the racial and political tensions building between the races.

Below the Root is a adventure game and a platform game. Choosing one of five characters (each very different from one another), the player explores the tree-based lands Erdling and the underground-based lands of the Kindar. As an adventure game, goals are primarily accomplished by talking to people (though each character is treated differently by others) and finding the right items to use in specific situations, but also dealing with the challenges of level design in a platform game.

Each character can obtain different items to help with their movement as well as psychic abilities such as pensing (telepathy), kiniporting (telekinesis) and grunspreking (plant manipulation). Violence is abhorred among the Kindar and the Erdling and violent actions tend to harm the player's reputation. Kindar or Erdling factions may kidnap the player's character if they wander into the wrong areas, throwing them into a local "prison house" from which they must escape. The player must eat constantly to retain their energy, however Erdling characters do not eat meat.