"Xenosaga: The Animation" is a 12-episode anime adaptation of the first game in the "Xenosaga" video game series, "Xenosaga Episode I: Der Wille zur Macht." The story is set in a distant future where humanity has abandoned Earth and colonized space, forming a galactic federation. The narrative centers on Shion Uzuki, a young scientist working for Vector Industries, who is developing KOS-MOS, a powerful android designed to combat the Gnosis, mysterious and hostile entities threatening humanity. Shion's life takes a dramatic turn when her research vessel, the Woglinde, is attacked by the Gnosis, leading to the activation of KOS-MOS, who displays extraordinary combat abilities.

As the story progresses, Shion and KOS-MOS are joined by a diverse group of characters, including Allen Ridgeley, Shion's colleague and admirer; chaos, a mysterious boy with a calm demeanor and hidden powers; Ziggy, a cyborg with a tragic past; and MOMO, a realian (a type of synthetic human) created to interface with the U.M.N., a vast information network. Together, they uncover a conspiracy involving the Gnosis, the U.M.N., and the Zohar, an ancient artifact with immense power. The group's journey takes them across various planets and space stations, where they encounter allies and enemies, including the enigmatic Albedo, a realian with a connection to MOMO, and Margulis, a high-ranking officer in the Federation's military.

The plot delves into themes of identity, artificial intelligence, and the nature of existence, as the characters grapple with their own pasts and the larger mysteries surrounding the Gnosis and the Zohar. Shion's personal struggles and her relationship with KOS-MOS are central to the narrative, as she questions the ethics of her work and the implications of creating sentient machines. The series builds toward a climactic confrontation with the Gnosis and revelations about the true nature of the Zohar, setting the stage for further developments in the "Xenosaga" saga. The anime condenses the complex lore of the game into a streamlined narrative, focusing on key events and character interactions while maintaining the philosophical undertones of the source material.