After the events in Ultima VI, the Avatar is transported by a friend's failed experiment with an obsidian "moonstone" to the otherworldly Valley of Eodon, a large jungle-like world filled with various tribes. These tribes have been magically drawn from varying periods and locations in history, such as the aboriginal nations of Mesoamerica and tropical Africa. The valley of Eodon is actually on Earth, but it is inaccessible and unmappable.

At the time of the arrival of the Avatar, the place is under attack from the insect-like Myrmidex. The Avatar needs to understand and master some aspects of their stone-age tribal culture and their "jungle magic" to find a way to bring peace to the valley. The main plot involves getting all thirteen tribes to join in an alliance against the Myrmidex. Each tribe has its own demands before joining, ranging from defeating a Tyrannosaurus rex to recovering their holy statue. This mixture of worlds was created by a huge corrupted moonstone that the Myrmidex possess, which has to be destroyed to prevent it collapsing in instability.