The story is set in 1966 in and around the American Yokota Air Base located in post-World War II Japan, a few months before the beginning of the Vietnam War. Its main protagonist is a girl named Saya, who hunts hematophagous bat-like creatures called chiropterans for a secret organization known as the Red Shield. Saya's mission begins in a subway train, where she assassinates a man suspected of being a chiropteran. However, David and Louis, her Red Shield contacts, arrive and discover that the man was not a chiropteran. David then gives Saya orders for her next mission. There are at least two chiropterans that have managed to infiltrate the air base, and it is only a matter of time before they feed again, go into hibernation, and become untraceable. Saya is to pose as a Japanese high school girl, infiltrate the high school adjacent to the base, and then track and kill the chiropterans. At the high school, Saya runs into the school's meek nurse Makiho Amano on the eve of the school's annual Halloween party.
Two of Saya's classmates, Sharon and Linda, make a visit to Makiho at the nurse's office. Suddenly, Saya bursts into the room and kills Linda and wounds Sharon, breaking her sword in the process. Both girls are revealed to be chiropterans. Makiho goes into shock at the revelation as Saya pursues Sharon. Meanwhile, a third chiropteran reveals itself and begins making its way to the base. Back at the school, Makiho regains her nerve and pursues Sharon, but is taken hostage by Sharon. She is saved by Saya and they both flee into a nearby motor pool. The chiropterans trap them inside and attack. Makiho manages to break down the doors with a jeep and faints. David then arrives and gives Saya a new sword, which she uses to kill Sharon. The final chiropteran then decides to flee, attempting to stow away on a departing cargo plane. David and Saya give chase and she manages to strike the chiropteran and mortally wound it. She then stands over the dying chiropteran and lets some of her blood trickle into its mouth, which apparently kills it.
Louis then arrives and recovers Makiho before the local police can reach her first. Afterwards, Makiho is seen at an interview with government officials who question her about the night's events. However, it's revealed that all evidence of the battle between Saya and the chiropterans has been covered up and both David and Saya have disappeared, leaving Makiho with nothing to prove the veracity of her story. Her interviewer then asks her to identify Saya in a picture which has a girl that looks identical to her, except the picture was taken in 1892. The only other description of the picture is the word "VAMPIRE". Makiho then returns to the school, where she narrates that she never really discovered the full truth behind Saya and the chiropterans, and wonders if she's still out there fighting them.
- Saya (小夜 Saya?) hunts chiropterans using a katana. It is implied that she is the last remaining vampire and called "the only remaining original." Saya has no weakness to sunlight, although it is unknown if she has any of the other vulnerabilities often attributed to vampires. She does, however, become distressed when she encounters religious paraphernalia and angry when people mention God in her presence. Saya displays superhuman senses and strength, as well as cunning, resourcefulness, and skill. The manga series suggests she was a human-vampire hybrid. Her age is unknown, but a picture of her with nine other people is shown in the film with the date 1892 and the word "vampire" attached to it. Though she holds most humans in contempt, she seems to have some sort of respect for David. Voiced by Youki Kudo.
- David is a man working for the U.S. government organization called the Red Shield. He relays the missions to Saya and helps her at various points in the film. Voiced by Joe Romersa.
- Chiroptera, Greek for "hand wings" and translated as 翼手 (yokushu?) in Japanese, are hematophagous bat-like creatures. They are extremely long-lived individuals that are comparable to humans in intelligence. Their natural appearance is much like a large, monstrous, long-limbed bat. Chiroptera live by feeding on human blood. They possess extraordinary speed, strength, and supernatural healing abilities and can heal almost instantly from any non-lethal wound. Because of this, the only way to easily kill them is to cause them to lose a sufficiently large amount of blood from one attack.