In the Battle of Toba-Fushimi in the next year, 1868, Naonori fought as the army of old bakufu but he seceded, and thereafter, Naonori joined the Meiji Government and moved from place to place to fight in the Boshin Civil War.
翌、慶応4年（1868年）の鳥羽伏見の戦いでは旧幕府軍として戦ったが離脱、後の戊辰戦争では明治政府に加わって転戦した。