The story begins when Ryudo is hired to protect Elena on her journey to investigate the return of the Evil God, a force that could destroy the world. Along the way, they encounter other characters like Maya and Sky, who add depth to their adventure, while also exploring themes of choice and sacrifice.

Xenosaga Episode III takes place after the events of Episode II, continuing the story in an environment filled with conflict between humans and interdimensional beings (such as the Gnosis) and the confrontation with The Zohar, a massive source of power that plays a crucial role in the world of the game. Shion Uzuki and her team of companions embark on a journey to uncover the truth behind the Gnosis and The Zohar, while also seeking a way to stop the threat posed by Albedo and the U-TIC Organization. Meanwhile, new characters like Ziggy and MOMO play significant roles in helping the main characters discover hidden truths about history and the universe. As the story unfolds in Episode III, players will witness a battle on a spiritual level and explore the meaning of existence. KOS-MOS is a character whose emotional development and key role in the story become crucial, as she is connected to The Zohar and is a pivotal figure in bringing the events to their 

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.

The story begins with Shion Uzuki and her team being sent to find and protect KOS-MOS, a robot developed to defend humanity from a threat posed by an enemy group known as the Gnosis, alien life forms that cannot be perceived by ordinary humans. During their journey, they encounter opposition from various organizations with the goal of exploiting robotic technology and conducting experiments that could potentially lead to the destruction of humanity. This includes the development of something called Uroboros and the creation of mutated humans. Additionally, the emergence of an organization attempting to control the universe philosophically is explored, with themes revolving around the use of religion and belief to manipulate the future, all while raising questions about "will" and the "meaning" of life in the universe.