The Spirit Realm in Ultima IX is supposed to represent the insides of the strangely regenerated Well of Souls. It essentially is a pocket dimension in which the restless spirits of various people have been locked in, since they were unable to grasp the true meaning of a virtous life but weren't outright evil.
The Avatar had to enter it in order to free Shamino. In order to do so, the hero had to get hints from the restless spirits where to find the three items that were essential in freeing the companion from his magical separation of body and mind.
- The whole concept with the Well of Souls being intact and the Spirit Realm directly contradicts Ultima VII, in which the well is explained quite detailed.