The Root (or Root System) is a theoretical living organism that connects all plant life in the Shivering Isles. It encompasses the hollow Root Tunnels that grow beneath the realm's surface, as well as the giant Mushroom Trees native to the Isles.
The tunnels, commonly called "root dungeons", grow at an incredibly slow rate, although it can vary from a few feet every month in places to only a few inches every few decades. Over the millennia, the system grew to cover the entire realm, and it is theorized that the tunnels acts as the veins of the realm, connecting every plant. The tectonic forces exerted on the Root results in the vast amount of amber deposits found in these tunnels, which is used by the mortal inhabitants of the realm to craft high quality weapons and armor. The Gnarl are said to be symbiotic caretakers of the Root, guarding the tunnels and cleaning up amber until they eventually fuse with the walls after growing too large. The tunnels often serve as homes for the various species of flora and fauna, and are regularly explored by adventurers. Entry is possible by opening the thin membranes at the base of giant Mushroom Trees.
Although heretical, it has been speculated that the Root acts as a conduit for the madness of the realm by transporting color from somber Dementia to vibrant Mania, and thus ecologically resulting in the mental illnesses of each region's inhabitants. Further, it is thought that destroying the Root and its Gnarl protectors would cure the realm's inhabitants and dethrone Sheogorath. This may have some semblance of truth, as the lifeblood of the Isles collects in the Pools of Madness in a root tunnel known as the Fountainhead, beneath the Palace of Sheogorath. These pools feed the Font of Madness, which would traditionally be corrupted by Order right before Jyggalag's arrival to take the palace at the end of each Greymarch.
Mushroom Trees and their saplings are capable of living on Nirn seemingly disconnected from the Root, as can be seen on Eyevea and the floating island in Niben Bay. The Root is similar in nature to the natural caves of Tamriel, which originally served as the capillaries of Nirn, pulsing with the divine essence of the Aedra. The Mushroom Trees are similar in appearance to the giant Emperor Parasol mushrooms of Morrowind.