Despite her harmless exterior, Yukari Marii, hides a deep, dark secret: her pretty purple eyes see all living beings as robots. Initially considering it to be nothing more than a quirky eccentricism, her friend Manabu "Gaku" Hatou soon realizes there's more truth to Yukari's words than she first thought. Despite her weirdness, Yukari's diminutive cuteness instills in Hatou a deep desire to protect her. In contrast, Yukari considers Hatou a "super-modifiable all-purpose robot."

Yet, Yukari's starkly unique view on the world has made her a lonely person, even causing her old friend Nanami Tenjou to act cruelly towards her. After an incident, Hatou finds out that Yukari is not the only one with a unique sight, termed a "Qualia." When Yukari is recruited into an institution for children with Qualia, Hatou is soon plunged into a conspiracy she must claw her way out of.