The Ω System ("Omega System") is a massive space fortress housing Proto Ω and the Original Zohar. Apparently, Ω System is an incarnated version of Old Miltia, for the planet was ripped apart from the inside out as the Ω System emerged. The Ω System has been fitted with many puzzles and locks to keep unwanted visitors out, as well as a pair of large guardian mecha (one of them taking the form of a full scale Cathedral). Proto Ω and the Original Zohar are housed in the core of the Ω System.
Shion Uzuki and her allies entered the Ω System to stop the Patriarch and his plot. However, after a stalemate battle (and a brief alliance with Albedo Piazzolla to take down the Patriarch), the three Testaments arrived to destroy the Patriarch. After this chain of events, Albedo morphed Ω System into a space-time anomaly for his own motives.
It is unlikely that the Ω System was man-made, but it can be inferred that it was created when the Patriarch, being a descendant of the Blood of Abraxas, communicated his will unto U-DO via the Zohar. U-DO, having complete and utter control over the Lower Domain, responded by metamorphosing the planet into a massive, mechanical citadel. Some of the enemies inside of the fortress appear also to be formed from this reassembly of the planet at the molecular level, similarly to Ω Res Novae's transfiguration in Episode III.
- Both the Ω System and the Proto Ω appear to be a collective homage to Deus from Xenogears. Although the Proto Ω itself is supposed to be the Zohar-powered, godlike super weapon (and indeed becomes more like Deus in appearence with each of its upgrades), the Ω System seems to be based on the massive outer shell that Deus sprouted once the Merkava had been shot down towards the end of the game, in order to protect its mobile weapon system, serving as the game's final dungeon. This version, however, unfahtomabily larger and in space. While the Ω System does serve a similar purpose in housing the Proto Ω, the two are not apart of the same weapon system, and the only link they share is their connection with the Zohar.