"Ray" is a 13-episode anime series that revolves around Ray Miyuki, a young woman with a tragic past and extraordinary abilities. After being kidnapped as a child and subjected to inhumane experiments, Ray gains the ability to see through objects and living beings using X-ray vision. This power, while useful, is a constant reminder of her traumatic experiences. The experiments were conducted by a shadowy organization known as the "Red Caps," which harvests organs from children to sell on the black market. Ray manages to escape their clutches and dedicates her life to dismantling the organization and rescuing other victims.

The narrative follows Ray as she works as a freelance doctor, using her X-ray vision to diagnose and treat patients while secretly investigating the Red Caps. Along the way, she encounters other survivors of the organization, including a young girl named Rie, who becomes a key ally. Together, they uncover the extent of the Red Caps' operations and confront the individuals responsible for their suffering. The series delves into themes of trauma, resilience, and the pursuit of justice, as Ray balances her desire for vengeance with her commitment to saving lives.

The main antagonist is Dr. Kōzaburō Takashiro, a former Red Caps scientist who played a significant role in Ray's torment. His cold, calculating demeanor and lack of remorse make him a formidable foe. Other characters include Dr. Kōjirō Amami, a compassionate physician who supports Ray in her mission, and Asuka, a mysterious woman with ties to the Red Caps who harbors her own secrets. The series explores the moral complexities of its characters, blurring the lines between hero and villain as Ray navigates a world filled with corruption and cruelty.

The plot is driven by a mix of episodic medical cases and an overarching narrative focused on the Red Caps. Each episode often features Ray using her abilities to solve medical mysteries while gradually uncovering clues about the organization's activities. The tension builds as Ray gets closer to confronting Takashiro and dismantling the Red Caps, culminating in a climactic showdown that tests her resolve and humanity. The series balances action, drama, and emotional depth, offering a compelling exploration of its central themes and characters.