An organic avatar functioned as a physical user interface to assist people, and once took on the form of the deceased Danny Pink using Clara Oswald's memories to help Clara and the Twelfth Doctor. According to the organic avatar, the "trees" were information servers, and the "rivers" were its data streams. The avatar also stated that the Jungle's creators existed in the memory of the Jungle. Clara thought they were "like ghosts".
At some point, the sentient superweapon the Hadax Ura came to the planet and was "devouring" the Jungle as part of its plan to turn the indigenous wildlife into an army to wipe out both the Hub Alliance and the Axis Worlds. (COMIC: Spirits of the Jungle)