Omega Metempsychosis is the ultimate and final configuration of Omega Res Novae. It serves as the last Omega boss when defeating Dmitri Yuriev and the post-transformed Omega. It virtually transforms into a powerful and formidable machine when Dmitri merges with it, along with the waveforms of U-DO that had infected him from his time of having direct contact with the entity. After Dmitri is defeated by Jr. and company, Albedo appears and takes the Zohar and Abel away from Dmitri and transports them to Michtam. It remained within Abel's Ark, as it served as one of the instruments for Zarathustra. It, along with the Gnosis and Abel's Ark, vanish when Chaos and Nephilim send all things back to Lost Jerusalem in the region of space.

It stands at the near size of its original form, much like the prototype before it. Like other mecha in the series, it is a recreation of a Xenogears design; in this case the Deus boss enemy from the end of the game. Where Deus sported two tiny angels, Omega Metempsychosis is accompanied by two E.S. look alikes attached to its arms; Omega Universitas and Elly's gear from Xenogears, Vierge.

The name "Omega Metempsychosis" is translated as "Omega spirit transmigration". According to the Xenosaga III database, back at the time of Lost Jerusalem, an Omega machine was also created which nearly resembles Omega Metempsychosis, but was presumed to have been destroyed when Lost Jerusalem disappeared as a result from the Zohar went out of control.