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.