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Purgatorium (ナラク) is a dungeon found in the series.
Latin for Purgatory. It is a place of temporary punishment or cleansing of those who will eventually be allowed into Heaven.
A special domain set up by Merkabah near the end of the game within the Hall of the Minotaur at Naraku to prevent any demons or the Unclean Ones from entering the Eastern Kingdom of Mikado, as the angels prepare to wage war against Tokyo. It appears as an endless sea of floating structures suspended in a vast sky. Purgatorium is divided into several "Crowns," which must be traversed on materializing walkways and by navigating a maze of teleporters that reverse Flynn's orientation, as well as barriers set up by various angels. At its summit is the Gates of Paradisio, where Merkabah stands guard.
In the Chaos route, Flynn and Lucifer break through the forcefield and enter Purgatorium to destroy God's chariot and invade Mikado. As they fight their way to the angels' barriers, Lucifer laments their almost robotic disposition and blind loyalty to heaven. At the Gates of Paradisio, they confront and defeat Merkabah. Lucifer denounces the chariot, asserting that the passions of demons and humans is what makes them truly alive, unlike the cold, machine-like nature of angels. As the Merkabah crumbles, Jonathan's voice can be heard one last time, asking if there's no end to their avarice. Lucifer will mention that one can pray to God all they want, but He will never answer. Stating that is God and with the threat of Merkabah gone, Lucifer reverts back into the form of Hikaru, and they continue to Mikado destroying the remaining angels that stand guard on the way.
In the Neutral route, in order to fully revive Masakado and remove the Firmament, Flynn and Isabeau must enter here and defeat Merkabah to recover the Great Spirit of Goodwill. As they climb through Purgatorium, Burroughs notes the machine-like behavior of the angel guardians. Upon passing through the Gates of Paradisio, they find themselves in a dark room. Jonathan's voice speaks to them, chastising them for rejecting God's affection, and insults them by calling them common stock. When Isabeau calls him out, he declares he is no longer the man they knew as "Jonathan," and reveals himself as Merkabah. The chariot declares that salvation is no longer open to them, and attacks. Upon defeating God's chariot, he warns that humans are not strong enough to live without the Lord, and those who yearn for their protection will arise again. Afterward, Isabeau paid her respects to Jonathan.