Proto Merkabah (known as The Wheel of Heaven in Xenosaga: The Animation) is a large space station created by scientist Joachim Mizrahi. Its surface function was to research and develop Realians, among other things. MOMO, the 100 Series Observational Realian, was also created in the heart of the facility by Dr. Mizrahi, but it was not the primary function of the facility. However, as Juli Mizrahi clearly explained, the Song of Nephilim was designed to dock with Proto Merkabah and the Zohar. The Song of Nephilim summoned the Gnosis, which were collected by Proto Merkabah (seemingly using the same technology employed by KOS-MOS when she performs X-Buster), then used as a medium to collect the waves from the Zohar as an energy source. Juli states that the original purpose of the facility was to "discover the true form of the universe; the form we ourselves were meant to have". The rogue U.R.T.V., Albedo, discovered that it could thus be used as a superweapon, and summoned Proto Merkabah from the Abyss as part of a three-pronged strategy. First, by establishing his power with the Song of Nephilim, summoning the station would draw Shion Uzuki and friends to the station. However, the incident would also harass the Second Miltian Government, and destroy the remaining Federation forces around Second Miltia. It was part of a grand plan to divert attention from the Immigrant Fleet and to the U-TIC Organization.

In Episode III, it is revealed that the U-TIC Organization used Proto Merkabah as a base for reconfiguring Realians. Ostensibly they were being treated for neurological disorders, but in fact they were being programmed to malfunction, causing much of the chaos during the night of the Third Descent Operation. It was also intended to be a mobile fortress for Proto-Ω, just as the Tactical Warship Merkabah became the base for Ω Res Novae fifteen years later.

Proto Merkabah was destroyed when Shion Uzuki and friends entered the massive facility in a bold attempt to stop Albedo. Using MOMO's schematic records of the station, the party quickly made it to the core, after facing powerful defenders like Proto Dora and hoards of powerful Gnosis on the reactor elevator. Unfortunately, after Albedo was defeated, he fused a massive Gnosis with the main reactor, spawning the deadly Sophie Peithos. During the confusion, he escaped. However, the facility was on course to crash into the capital of Second Miltia. In a calculated gamble, KOS-MOS offered to stay behind and break Proto Merkabah into tens of thousands of compartments, thus allowing the bulk of the station to disintegrate in the atmosphere. KOS-MOS narrowly made it back to the Elsa as it escaped the crumbling space station just in time. The plan succeeded, and Proto Merkabah was destroyed and the compartments burned harmlessly into the atmosphere of Second Miltia.

In some of the promotional trailers for Episode III a massive space station closely resembling Proto Merkabah can be seen. This station appears to have a much sharper and smoother base, and is a related base simply named Merkabah. Merkabah is being constructed by the Galactic Federation in orbit of Fifth Jerusalem and has some sort of relationship to the war on the Gnosis.

"Merkabah" is a term used by Kabbalists to refer to a mystical inner journey undertaken through which one could see the full glory of God. Merkabah is also known as the "Chariot of God" and an allusion to Deus' transportational system in the game Xenogears, which is in line with the many references established between the games.