Silent, apathetic, yet mischievous, 14-year-old Rokujou Miharu is the bearer of the hijutsu, "Shinrabanshou," a powerful technique many ninja clans desire to possess to become the ruler of Nabari. Fellow classmate Kouichi and his English teacher Kumohira are both secretly Banten clan ninjas, pledging themselves to protect Miharu from his many attackers. Keeping apathetic, Miharu attempts to reject their invitation to join their ninja "club." However, after numerous attacks, he finds no choice but to join their group as a means for his survival. Slowly, Miharu takes a step closer to becoming the ruler of Nabari. [Written by MAL Rewrite]

While in search of his precious friend, a young boy named Nai falls captive to a beautiful woman, whose looks are matched only by her taste for human flesh. Meanwhile Gareki, a clever thief, is in the midst of robbing her luxurious home. After causing a distraction, Gareki agrees to help Nai escape, but they are discovered upon the woman's return. As she transforms into a ghoulish monster, the boys flee. On the run, Nai and Gareki are found by "Circus," a government defense agency that deals with criminal activity too difficult for the police to handle and protects civilians from "varuga"—terrible monsters that devour humans for sustenance. In the hope that it will lead Nai to his missing friend, he and Gareki decide to join Circus. On their perilous journey, they face dangerous varuga and begin to uncover the secrets behind a shadowy organization known as Kafka. [Written by MAL Rewrite]

A two-episode special. They are designated as Episodes 13 and 14, and the first episode is a direct sequel to the previous series while the second episode is about the trans-sex of Natsuru.

During the dawn of the 21st century, the United Nations Kurobe Research Institute was established in Japan to investigate an ancient artifact, which was discovered during the construction of the Kurobe Dam. Scientists from around the world have gathered in the facility to study the object, while their children enjoy their everyday lives attending Mt. Tate International Senior High School. Yukina Shirahane, a reserved high school girl, is the daughter of the facility's head scientist. While visiting her mother at the facility, Yukina manages to solve part of the artifact's puzzle. To her surprise, what appears before her is Kennosuke Tokisada Ouma, a young samurai from the Sengoku era. As a threat approaches from outer space, Yukina, along with Kennosuke, finds herself defending Earth against the invading forces. Along the way, she discovers the mystery behind Kennosuke and the reason he is determined to protect her. [Written by MAL Rewrite]