"Sci-Fi Harry" is a supernatural mystery manga that blends elements of science fiction and horror. The narrative centers on Harry, a high school student with a mysterious past and the ability to see ghosts. After moving to Japan, Harry becomes entangled in a series of bizarre and often deadly events involving supernatural phenomena. His unique ability draws the attention of both malevolent spirits and a secretive organization known as the "Science Agency," which investigates paranormal activities.

The story unfolds as Harry encounters various supernatural entities, each tied to unresolved human emotions or tragic events. These encounters often lead to dangerous confrontations, forcing Harry to confront his own fears and uncover the truth about his origins. The Science Agency, led by the enigmatic Dr. Kuroki, plays a significant role in the narrative, as they seek to harness Harry's abilities for their own purposes while also protecting him from external threats.

Key characters include Harry's classmates, who become involved in the supernatural occurrences, and Dr. Kuroki, whose motives remain ambiguous throughout much of the story. The manga explores themes of loss, redemption, and the blurred line between science and the supernatural. As the plot progresses, Harry's past is gradually revealed, shedding light on the source of his powers and his connection to the Science Agency. The series maintains a tense atmosphere, with each arc building on the mysteries surrounding Harry and the world of the paranormal.