At the end, with the other 18 participants dead, Oboro and Gennosuke face off in the last battle. Fortunately, Gennosuke cannot bring himself to kill Oboro, and Oboro cannot kill Gennosuke, so Oboro kills herself, thus ending the cycle of hate. Gennosuke then takes revenge on everyone before following Oboro in suicide. The episode as well as the anime ends melodiously / romantically. The long waited peace is finally achieved.
In the end as Gennosuke and Oboro float off in the river, the scene is reminiscent of Danjou and Ogen's last scene together near the beginning of the series, however the main and biggest difference is that Danjou and Ogen kill each other because their hate was greater than their love, while Gennosuke and Oboro cannot bring themselves to kill their beloved. Thus, Gennosuke and Oboro end the cycle of hatred between their clans.
As a post-credits scene Hattori Hanzo the 4th was so moved by their sacrifice that he would later negotiate a new peace between their clans in which the promised spoils were evenly distributed among them both. He also recovers the battle scroll from Lord Ieyasu and secures it in a secret alcove of his manor so that the memory of the twenty chosen ninja would not be completely lost to time's passing. His adopted son Kyohachiro takes Gennosuke's flute (which Oboro had told Kyohachiro to hold onto for her) with him to Aekuni Temple where he will present the flute as an offering. As he walks he makes a promise to the both of them that he will never forget them or their legacy for the rest of his life.