Xenosaga Episode II continues to be part of a deep and complex sci-fi narrative, which involves the struggle between humans, AI, and other life forms, particularly focusing on "The Zohar," a mysterious power that influences everything in the universe. The story of Xenosaga Episode II takes place after the events of Episode I and centers on the development and search for the truth related to "Gnosis" (mysterious beings capable of destroying humans), as well as uncovering answers about "The Zohar" and the "U-TIC Organization," an entity involved in these events.