In 1867, he worked with French Army officer Jules Brunet to mobilize all Assassin agents in Japan to ensure the victory of the Tokugawa and their allies over the Templar-backed Imperial Court. Matsuo then met shinobi Issa to discuss the recent abdication of Tokugawa Yoshinobu from his title as shōgun. He was reluctant to allow him to assassinate British Consul Harry Parkes since the latter believed that if he was killed, the British Empire wouldn't support the Emperor and his allies. However, Matsuo was convinced otherwise and he would send Issa to assassinate Parkes, a mission that ended in failure since British Templar William Lloyd would kill him with his firearm.
Angered by the Templars killing Issa, Matsuo infiltrated the personal battalion of Lloyd by disguising himself as one of his rōnin, "Masajiro". Matsuo later encountered Nakano Takeko's protégé Shiba Atsuko during an assault on the enemy camp, but was spared as the latter chose to kill the soldier battling her mentor instead. He met Atsuko once again after the Battle of Aizu, offering her the opportunity to join the Assassins citing the deeds of her brother Ibuka saving her from death and preventing the Musashi Masamune from falling into Templar hands. Despite the Imperial victory over the shogunate forces, Atsuko eventually joined the Brotherhood, much to Matsuo's delight.