The organization was founded by Utsuro about five hundred years ago, working under the control of the Bakufu. It is unknown what happened to the cult after they were dismissed in the beginning of the Tokugawa Shogunate after they were replaced by the Oniwabanshuu. Although it is implied that lesser government officials turned to them for assassinations. From the moment of the Amanto's arrival twenty years before to the present day, the group works under the Tendoushuu. The Naraku's former leader, Utsuro, has become a member of the Tendoushuu. Oboro was the current leader until his death, leading to Utsuro gaining control of the Naraku once again.
The Three Wings of NarakuEdit
The Naraku is introduced as working for the Tendoushuu and were protecting Tokugawa Sada Sada by their orders. Imai Nobume reveals some of their history while Sada Sada reveals that they were involved in the Joui Wars' Kansei Purge by helping to gather dissenters and were the people responsible for the arrest of Gintoki, Katsura, and Takasugi's teacher, Yoshida Shouyou. Their leader, Oboro also has a history with Gintoki as they fought each other during the wars but before Oboro was the leader. The Naraku and Oboro nearly overwhelm the combined forces of the Yorozuya, Tsukuyo, and Nobume until the arrival of the police forces lead by Sada Sada's nephew, Tokugawa Shige Shige. Gintoki is able to defeat Oboro and the assassins were forced to flee with the Tendoushuu, leaving Sada Sada behind to pay for his crimes.
It is later revealed the Nobume was a former Naraku and Oboro gains a strange interest in Shouyou's students, especially Gintoki and Takasugi.
Nobume reveals some information on the Naraku's former boss, Utsuro. The man was also responsible for making Oboro semi-immortal, explaining how he survives his on-screen deaths. The Naraku work with the Harusame due to Utsuro having control of both to wipe out Utsuro's enemies. They retreat with Utsuro after the immortal got what he wanted (his fight with Umibouzu along with distracting the Tendoushuu). Oboro chooses to stay behind and is finally fatally wounded by Takasugi. He reveals to Takasugi more of Utsuro's past and his plans along with Oboro's own involvement with the immortal.
Utsuro now uses them for his plan of Earth's destruction. He gives them his blood, making them semi-immortal and has them attack multiple outposts of the Altana Liberation Army as well as Nobume and the Yorozuya, disguised as civilian. This will make both sides believe that Earth has broken the temporary truce and will lead to Edo being conquered.