Yukari Marii, with her innocent facade, holds a hidden secret: her enchanting purple eyes perceive all living beings as mechanical entities. Initially brushed off as a peculiar trait, her companion Manabu 'Gaku' Hatou soon realizes the profound reality behind Yukari's perceptions. Despite her oddity, Yukari's adorable smallness sparks a protective instinct in Hatou. Conversely, Yukari views Hatou as a 'super-customizable, multi-functional robot.' However, Yukari's unconventional outlook renders her isolated, leading even her former friend Nanami Tenjou to treat her harshly. Following a revealing incident, Hatou discovers that Yukari is not the sole possessor of a unique sight known as 'Qualia.' As Yukari gets enrolled in a facility for Qualia-endowed children, Hatou is thrust into a labyrinthine conspiracy that demands her escape.