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Zarathustra as seen in Episode III.

Zarathustra is the final boss and namesake of Xenosaga III. Powered by the Original Zohar and the power of the awakened twelve Vessels of Anima (the combined power of half of the Anima, Yeshua, which was sealed by the Animus, Mary, during the Lost Jerusalem era to delay the universe's destruction), it is found deep within the planet Michtam. In fact, it was created by the ancients of Lost Jerusalem and moved by the Immigrant Fleet to Michtam.

According to the Episode III database, Zarathustra itself is a series of crystalline structures; its control panel resembles the Compass of Order and Chaos on a gigantic scale. Zarathustra was originally built by the ancients as a means to transcend to the realm of God and become gods themselves. Wilhelm, however, uses Zarathustra as the central device in which to constantly repeat an "eternal circle" of time. This reverses the dispersal of consciousness by literally reversing time back to the beginning and temporarily channeling the consciousnesses through imaginary time. Because of this, people relive the same lifetimes and history repeatedly. Wilhelm uses his "temporal recurrence ability" with the Vessels of Anima, Abel, the Zohar, Mary Magdelene (reborn within KOS-MOS) and the "Key" (Shion's pendant) as the components to start Zarathustra and complete this process. However, after numerous recurrences (the database does not clarify how many), the human will began to reject the constant process due to the distortions made each time Zarathustra reset time, and thanks to the intervention of Kevin, the Red Testament and Wilhelm's own right hand man, his link to the Zarathustra device and Abel was severed, and they went out of control. Zarathustra merged with Joshua (Wilhelm's mecha, and piloted by an out-of-control Abel), and began tearing off parts from all twelve discarded E.S.s, as well as mutilating itself and attaching the body parts of the E.S.s to itself. The large, golden "compass" that held the Original Zohar, the rings of Order and Chaos attached to the frame of the "fused" Joshua as well. When it is "complete," the party faces off against the monstrosity, but it is eventually defeated after a long and difficult battle. Abel (U-DO's human form) returns to normal after U-DO decides to give humanity the chance to live on.

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