The story takes place in the near future, and describes a young girl living in an institution that raised children in order to sell their organs on the black organ transplant market. This girl, who had christened herself "Ray" because the numbers (075 - 1 - 74) on her back used to identify the children equal zero when subtracted, since Rei is the Japanese word for zero. After losing her original eyes she was rescued and outfitted with a pair of new X-Ray eyes by the underground doctor Black Jack and was adopted by a surgeon named Dr. Kasugano. Upon receiving her sight back Ray was told that her life was now hers to live as she wished.
Ten years later Ray has taken up her mother's profession and become a well known and respected surgeon because of her unique abilities and sharp skill. After beginning work at a less-than-typical hospital, Ray is faced with bizarre cases that require her specials skills; ranging from a dangerous pathogen that requires her to perform surgery underwater to a girl seemingly possessed by a malignant entity. In the second half of the series she begins to uncover details about the organization that removed her eyes and the whereabouts of the other children she was raised with, and the storyline takes up bioethical issues such as organ donation, human cloning and even reincarnation.
Like its counterpart Black Jack, the show favors science-fiction elements in place of realism, with cases often resembling actual medical conditions but with fantastical elements added to heighten drama.