Robin Sena is a "craft user", born in Japan and raised by the Roman Catholic Church in Italy. She is trained to use her craft (fire) to hunt down witches. Witchcraft is a genetic trait, dormant within a number of individuals within the human population. Powers can be "awakened" in these dormant human "seeds" at any time. Trained hunters, craft-users or "seeds" themselves, are needed to keep watch over "seeds" and hunt those whose abilities become active, serving in secret organizations, such as the parent branch "Solomon" (and the "STN-J" branch in Japan), as self-appointed witch police to curtail the use of witchcraft in society, and to keep the witch kind in secret from the public. Even the police, who cooperate with STN-J in abnormal criminal cases, do not know what STN-J does.

The series begins when Robin arrives in Japan to gain information for Solomon headquarters about a fabled item that holds the "secrets of the craft", while acting undercover as a new hunter to the STN-J in their efforts to capture witches. It is hinted that she subconsciously understands something of the STN-J's use of Orbo.

Orbo is a green liquid that negates witch abilities. STN-J's hunters carry small vials of it on necklaces as a form of protection against their targets' craft. Hunters also carry air pistols which fire darts or pellets of orbo that dampen witch powers when it enters the bloodstream of the target witch. Hunters who are craft-users or seeds can use orbo with little ill effects (their powers are reportedly diminished while using it). Robin, a craft user herself, says that she will not keep orbo on her because it "frightens her."

As the series goes on, Robin grows increasingly uncomfortable with her role in hunting and capturing other witches. She begins to question the treatment they receive while incarcerated in the mysterious "Factory". After the discovery of "secrets of the craft," she was entrapped and attacked twice by "witch bullets". Aside from that, STN-J is attacked, presumably for "secrets of the craft" (though as it turned out, the last attack was Solomon's attack to find out what Zeizen was planning).

Robin begins to worry that she will become a target and grows to suspect that her partner Amon would hunt her. Eventually, Robin does become a target of Solomon and labeled a witch, becoming "hunted". In the end, Robin finds out more about her craft and that of witches than she knew at the beginning.

Initially, the series appears to take a "monster of the week" approach. About halfway through the 26-episode season, the characters and the relationships between them are established and the main plot gets underway.