Mitsunaga, however, sided with the Retired Emperor Goshirakawa when Yoshinaka became antagonistic to Goshirakawa, and stood up together with Yukitsuna TADA of the Tada-Genji to defend the Imperial Palace as main forces of the Retired Emperor's army at the time of the Battle of Hoju-ji Temple in November 1183, but he was killed in action together with his son Mitsutsune after the fierce fight, with his severed head exposed to the public.
しかし、義仲と後白河院の関係が悪化すると院方に付き、同年11月の法住寺合戦では多田源氏の多田行綱らと共に院方の主力として御所の防衛に当たるが、激闘の末に子の光経共々討ち取られ梟首された。