okay, so the story begins in present day Pharm with delinquent ninja students Ohga and Yuri hanging around. They summon the long-dead spirit of Miyuki and you hear about her history. So in ancient times, Pharm was ruled by Jiraiya (his wife being Chizuru and children being Hayate and Miyuki), with Kaede being a member of the royal family. Jiraiya favours Miyuki as a ninja and entrusts her with Sakurafubuki.

Then one day, Miyuki gets poisoned/mind-controlled by Otogiri, a salve-maker spy from another kingdom entrusted on a mission to overthrow Pharm. Miyuki ends up murdering Jiraiya as a result of being mind-controlled, and gets killed off by the poison. Chizuru commits suicide with the assistance of Hayate as a result of her failure to protect her family and losing honour.

In the end, Pharm is overthrown by Otogiri's people. In the present day, Yuri and Ohga reconnect Miyuki with the spirits of her family and she is grateful. Yuri and Ohga decide to summon Otogiri to learn more about her motives, and since Ohga is a descendant of her (living peacefully in the present day kingdom of Pharm). Otogiri explains that while her actions were inexcusable, overthrowing the poorly-defended monarchy of ancient Pharm enabled them to establish a peaceful democratic society, so Yuri and Ohga can live fulfilling lives. So uh, sacrifices and the greater good. and stuff