The Encephalon ("brain" in the Greek language) is a massive, virtual reality world normally accessed through the assistance of special red goggles. However, it is implied that the goggles don't serve any visual purpose and, instead, aid in connecting to the brain.
The goggles can also be compared to Oculus Rift or PlayStation VR, but the Encephalon is so advanced that a user can access it with their eyes closed and still be immersed in the virtual world. As such, it is similar to having an extremely realistic lucid dream.
The Encephalon can recreate locations in absolute detail. However, in some cases, this may have an affect on the brain; whatever happens in virtual space can still affect the body’s state in the real world (similar to The Matrix). The Encephalon is extremely realistic and complex, almost as if it is another dimension on its own.
Encephalon dives are often connected to the U.M.N. This is why it's possible to encounter Gnosis in the Encephalon, as the U.M.N. uses the Collective Unconscious as a network infrastructure. Gnosis exist in the same region, namely, the imaginary number domain, and so this is why the Gnosis encounter rate is high within the U.M.N. and Encephalon.
A "disconnect" refers to the act of physically breaking one's connection to the Encephalon within the U.M.N. when trouble arises during the session. Although it depends on the connection system, in most cases the subject will suffer significant physical damage; in the worst case, his or her brain may even become impaired. For this reason, disconnects are usually prohibited.
This is also why if someone dies in the Encephalon (by a Gnosis), they also die in reality and the player is given a game over.
Shion Uzuki and friends encounter many strange people and events in the Encephalon. The Encephalon changes depending on the person's mind.
Nephilim Verum, Febronia, and many other enigmatic figures seem to exist in the Encephalon, as seen through the minds of KOS-MOS and MOMO Mizrahi. These figures seen in the Encephalon have some sort of connection to the Zohar.
Encephalon dives serve as the player's method of revisiting previous areas, allowing them to battle lower-level Gnosis and other targets as well as retrieve lost treasure.
- In Xenosaga: The Animation, it is revealed Pellegri can Encephalon dive in E.S. Issachar while Issachar auto-pilots itself.
- In Xenosaga: Pied Piper, a risky Encephalon dive is performed into the mind of a dead man (Klaus Torres), since they theorized that the brain cells take a while to die.