The Zohar Incident was a mysterious interplanetary conflict which ultimately led to the events of the Miltian Conflict. According to Xenosaga I&II, it started when the autonomous planet, Zohar, began invading the autonomous planets of the Miltian System. There was never an official declaration of war, and the entire truth of what really happened was lost due to the space/time anomaly which engulfed the region afterwards.
Among the rumored causes, were that extremists among the people of the Immigrant Fleet who lived chiefly among the planets of the Miltian System and Zoar, had feared Miltia joining the Galaxy Federation. Another rumor was that the Federation's Salvator Faction had orchestrated events by posing as extremists, for the sake of taking control of the Miltian System by occupation. In any event, the conflict erupted into a power struggle between the Federation's forces and the Immigrant Fleet's military arm, U-TIC.
Zoar is yet another Biblical reference. In the story of Lot, after escaping the destruction of Sodom, his family rested in the city of Zoar.