|“|| Jin, you are exceptional. But your strength means that you will always be alone in this world.
In Episode I, very little is known about him aside from the fact that he pursues the Y-Data hidden in MOMO's subconscious, he wields a sword with spiritual abilities, and that he is commander of the U-TIC Organization. His associates as introduced in Episode I were his second in command, Pellegri, Andrew Cherenkov, a misfit Super Soldier variant, U-TIC scientist Sellers, and the rogue U.R.T.V. Albedo Piazzolla.
With the development of Episode II, Margulis' role is increased. Both forceful and arrogant, he cares little for the lives of those sacrificed by his actions, whether civilians or his own operatives. In Episode III it is revealed that he has a black-plated E.S. with a large broadsword and two wing-like drones.
During the Miltian Conflict, 14 years before the events of Xenosaga Episode I, Margulis was a double agent serving as a Colonel in the Federation Military and working for U-TIC and the Ormus Society at the same time. One of the soldiers under his command, Jin Uzuki - Shion Uzuki's older brother - had discovered his treachery and was going to use the Y-Data to reveal his and his superiors' dealings to the proper authority. Before he could do that, Margulis confronted Jin and the two engaged in a heated sword fight which resulted in Jin giving Margulis the sword scar that appears on his face in the game's present-day timeframe. Later, it is revealed that both men were actually taught by Jin Uzuki's grandfather in the ways of martial arts, swordplay, and Ether manipulation. Jin claims that Margulis "betrayed" his grandfather, but what he meant by that is not explicitly known. He could have meant betrayed him on principle by siding with U-TIC and becoming a criminal, or perhaps Margulis played a role in the old man's death. Either way, Margulis' betrayal is one of the major driving forces behind Jin Uzuki's pursuit of Margulis and, ultimately, Ormus and the mystery behind the Miltian Conflict and the Zohar.
After the U.R.T.V. Albedo stole the Y-Data from MOMO's subconscious, the U-TIC Organization and their allies (or one might argue them to be their leaders) the Immigrant Fleet made a raid on the planet Old Miltia to gain possession of the Original Zohar, now unlocked with the Y-Data. Once there, another personal duel between Jin and Margulis ensued. Upon being defeated, he exclaimed that it would be too late to stop the plans of using the Zohar, since the Zohar was already in the possession of the Patriarch. With Margulis' plan set in motion, he supposedly abandons the Patriarch to be killed by Shion and friends in the Omega System, so that the Patriarch would be replaced by Heinlein, and then Margulis would obtain more power. Margulis was in on this because Heinlein, Sellers, and Margulis are all connected to a project involving Hyams, which the Patriarch has no knowledge in. In other words, Margulis, Sellers, and Heinlein have their own motives that will be revealed in Xenosaga Episode III.
Margulis' motives, as revealed in Episode III stem from the fact that he believes Sergius to be a petty and foolish old man who has lost sight of Ormus' original goal, returning to Lost Jerusalem. He believes the Heinlein shares this ideal and follows his orders unquestioningly because of it.
At the beginning of Episode III, Margulis reveals that he is one of the "people of the Zohar", born on planet Michtam, also known as Abraxas, what he believes to be the birthplace of Ormus. He believes that the Immigrant Fleet's return to Michtam is a sign of the beginning of their return to Lost Jerusalem. However, doubts begin to form in his mind when Heinlein begins issuing orders that seem to contradict Ormus' goals. He follows these orders with a measure of reluctance right up until the end of the game when Heinlein orders the fleet to abandon Michtam. When he shows his stubborn dedication to the ideals of Ormus, "Heinlein" realizes there is no helping him. He steps forth finally and reveals his true form to his devout disciple; Wilhelm of Vector.
When Wilhelm explains Ormus' true purpose to Margulis, to protect the "words of God" (Lemegeton) and the "relics of God" (The Zohar, Zarathustra, the Anima, et. all) he questions whether or not everything he had worked for was all in vain. He then questions his own faith before coming to terms with the fact that a return to Lost Jerusalem is indeed impossible. He fights Jin Uzuki and everyone else in the E.S. Levi one last time. After being defeated and with his E.S. close to the point of self-destructing he claims his own life with his sword, not wanting to give Jin Uzuki the "satisfaction" of killing him.