Zarathustra is the final boss and namesake of Xenosaga Episode 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 Magdalene, 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, Eternal Recurrence. 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. With the intervention of Kevin Winnicot, Wilhelm's link to the Zarathustra device and Abel was severed, and they went out of control. Zarathustra, piloted by an out-of-control Abel, merged with Joshua (Wilhelm's mecha) and began tearing and attaching parts from all twelve discarded 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. This monstrosity was defeated by the party in a long and difficult battle. Following its defeat, Abel returned to normal and decided to give humanity a chance to live on.