Ga-rei

The Japanese Ministry of Defense's Paranormal Disaster Countermeasure Headquarters is summoned to eliminate Kashas in the Greater Tokyo Area by deploying its 1st and 4th Divisions into combat under MOD instructions after reports of a supernatural presence were sent to the MOD, with the situation under SDPH jurisdiction. Initial efforts by soldiers of the 1st Section seemed successful before they were being overwhelmed by demons in the highway. Toru and Natsuki of the 4th Division intervened to save the remaining survivors. Despite being able to kill the Kasha beasts after the 4th Special Division lured them into well-arranged traps, most of the PDCH operatives were either massacred by the transparent spirits or by a katana-wielding woman.

The Ministry of Environment's Supernatural Disaster Countermeasures Division, under the command of Ayame Jinguuji, intervenes after numerous PDCH casualties were reported by the Ministry of Defense; among the SDCD operators deployed for the mission included high school student and katana user Kagura Tsuchimiya. Corpses of 1st Special Division commandos were mysteriously alive after being killed, forcing SDCD operatives into action in order to kill them. The katana-wielding woman was revealed to be Yomi Isayama, an ex-SDCD operative who had somehow been corrupted and gone renegade.

A flashback episode. Kagura was placed under the care of the Isayama family at a very young age when her father had been using the Ga-rei Byakuei to battle various paranormal forces in Japan by himself after her mother had passed away, killed in action by a white-haired boy. Here, Kagura bonds with Yomi Isayama, the two later being good friends eventually and a secret agent of the Supernatural Disaster Countermeasures Division. She first encounters the SDCD field team led by Kouji Iwahata, a veteran SDCD operator. During Kagura's time with the Isayamas, Yomi helps her overcome being homesick from her home and her deceased mother.

Yomi and the other SDCD operatives are dispatched to eliminate a Tsuchigumo roaming on the countryside; Kagura makes her debut after saving a woman from being crushed by the Tsuchigumo's corpse. A civilian, however, witnessed their entire operation, later leading to an encounter between the woman and the entire SDCD team. Yomi and Kagura are dispatched to an old subway system when they encounter the same woman, now a vengeful zombie with a cadre of people killed by her back in the subway. Kagura's father arrives to save her by using the Ga-rei spirit Byakuei after showing several signs of hesitations of killing the zombies due to her insistence that they were still people.

Yomi is officially engaged to Nori, despite objections from her foster uncle on the matter itself as she had been adopted into the Isayama family. Yomi and Nori get into an argument due to her use of cosmetics and perfume as the two had nearly used their spirit beasts against each other without thinking of the safety of their comrades, forcing Kagura to come up with a plan to reunite them with help from the entire SDCD division before the two could end their engagement for good permanently, including Ayame being in on Kagura's plans herself. The two immediately got back together after Kagura confesses to them her intentions.

Reports of Category D monsters and a Yamabiko had appeared in the Greater Tokyo Area from SDCD intelligence. The SDCD, in response, had decided to covertly mobilize all available personnel to deal with sightings of monsters in the capital, including Yomi and Kagura. Kazuhiro Mitogawa appears before Mei after she dispatches some demons before the white-haired boy kills her after revealing his Sesshouseki that took the place of his real eye on his left eye socket. Kagura is forced to kill her high school infirmary doctor in horror after being possessed by a mind controlling demon before she could kill her classmates.

Kagura is given time off by the SDCD by Ayame under Kiri's recommendations due to PTSD after killing the middle school doctor in the previous operation, whose death has also been covered up by the SDCD from the rest of the public due to the involvement of the paranormal in her death as well as with "her" victims. Witnesses to the doctor's death, who had been Kagura's classmates, scold her for her actions until she told them why she had to do it. Yomi is also given some time off to console Kagura. One night, Yomi's adopted father was murdered by an unknown assailant in the Isayama residence, being caught off his guard.

After the death of Yomi's adopted father due to his serious injuries from being attacked by the unknown assailant, Yomi's foster uncle takes control of the head of the branch family and decides that Mei will become the exorcist and Yomi is forced to hand over Shishiou to him. Nori tries to track down the assassin who murdered Yomi's foster father while rift grows from the Isayamas over who should really inherit the control of the family as anti-demon exorcists. Mei is told by Kazuhiro that he had given her a Sessh?seki after being killed. Later, Yomi and Mei face off in a life or death match where everything comes to light of recent events with the revelation of Mei being the assassin herself. In anger, Yomi kills Mei with her naginata.

Yomi becomes incapacitated after an attack by Kazuhiro during an encounter in a local park to follow up on the lead of Mei being possessed by the Sessh?seki before being rescued and treated in a nearby hospital. The wounded Yomi is accused of murdering Mei due to her inheriting the position of being the top anti-demon exorcist in the Isayama family and being told the bad news on Nori. Yomi loses everything due to this and Kazuhiro reappears again in her room to offer a deal for her restored life during a visit when he gives her a Sessh?seki for her to use. Afterwards, she turns up missing from her hospital room when Kagura comes to check on her.

While Yomi goes missing, Kagura and the others are called on to take on the kashas in the Greater Tokyo Area without her help with the SDCD on the scene as the PDCH try to attack a kasha by themselves. Noriyuki investigates the attack on Yomi and comes to a conclusion that some person is pulling the strings. As Kagura and the others finish their job, Yomi appears, as the mysterious assailant. As Yomi flees, Kagura and Noriyuki give chase to her, in which, Noriyuki confronts Yomi, but cannot find the strength to kill his supposed fiancé as he watches Yomi kill Kazuki without any remorse after she captures him with Ranguren in the streets. As Yomi corners Kagura, a mysterious figure comes to Kagura's rescue and faces Yomi.

After her father is mortally wounded by Yomi in an attempt to rescue her even with the use of Byakuei, Kagura stays by his side as he slowly dies, having a heart-to-heart conversation with him for the first time. Meanwhile, the remaining members of the SDCD decide to confront Yomi directly themselves in an industrial area led by Ayame and Kiri with disaster on the SDCD operators despite having superior numbers when they fought Yomi. After her father passes, Kagura inherits the Sesshouseki from him and receives a new sword from Michael: Michael 13 before she sets out to take down Yomi herself and eliminate the threat of the Sessh?seki in her body.

Once the SDCD discovers Yomi's current position, Kagura and the other surviving SDCD operatives decide to pursue and stop her once and for all as the remaining PDCH and SDPH operators move in to assault Yomi and take her down. Though Yomi eventually gains an upper hand in her fight with Kagura, she is temporarily stopped by Noriyuki who helps Kagura retreat after being wounded. After retreating, Noriyuki bandages Kagura up and convinces her that Yomi is no longer the person she knew; Yomi, in the meantime, struggles to gain control over will. As Yomi and Kagura meet again and fight for one last time, Yomi is finally able to give in and allow Kagura to kill her. Two years later, life continues on for those involved in the ranks of the SDCD, and Kagura prepares to face a large ghost at the Tokyo Tower with her new partner Kensuke Nimura.