Daimyo of Aizu Katamori Matsudaira (Hideaki Ito) is appointed to the unfamiliar position of Kyoto Military Commissioner and then goes through the Boshin War. "Byakotai" depicts seven years, from 1862 when the tragedy begins to 1868.
In the last days of the Edo period, chief senior councilor of the of Aizu, Tanomo Saigo (Kinya Kitaoji) lives frugally and happily with his wife Chieko (Hitomi Kuroki), his parents, brother and children. He also trains young boys. Things change in 1862, when Katamori Matsudaira is appointed as the Kyoto Military Commissioner. Around this time, the Tokugawa shogunate's dignity means very little, with ronins of Sonno joi gathering in Kyoto. Consequently, public order and security crumbles in Kyoto. Under this situation, the Tokugawa shogunate creates The Office of Kyoto Protector to regain control of the area.
Tanomo Saigo strongly suggests that Katamori Matsudaira should turn down the position, due to the bad financial situation of Aizu. Even though Katamori Matsudaira is physically ill, he nevertheless leaves for Kyoto. Katamori Matsudaira leads a crack down on the ronins of Sonno joi. Katamori Matsudaira makes enemies in the process and becomes involved in a chaotic political sitation.