Despite his refusal to follow orders when he was recalled to France after the abdication of Tokugawa, he still became a General and Chief of Staff of the French Minister of War by 1898.
In 1867, Brunet was sent by Emperor Napoleon III to Japan with the French military mission to assist the shōgun Tokugawa Yoshinobu in his efforts of modernization of the Japanese Army. During his time in the archipelago, Brunet also acted as the liaison between the European Brotherhoods and their Japanese brethren.
In August, Brunet advised Yoshinobu about the Icarus affair in the shogun's private quarters in Edo, assuring him of the Brotherhood continuous support. While Brunet pushed him to stand his ground, Yoshinobu wanted to concede as the British demands were backed by the Emperor. The discussion was cut short, as the Assassin sensed the presence of someone else in the room. Despite Brunet's quick reflexes, the spy was able to escape through the window. Eventually, Yoshinobu decided to bow down to all the demands of the Emperor and by November, even abdicate his title of shogun.
Some time later, Brunet tasked his Japanese contact, Matsuo, to mobilize all his agents on the island in order to ensure the victory of the Tokugawa clan and their allies as the war became inevitable. The Frenchman was furious, as all his efforts to influence Yoshinobu toward a fairer and freer Japan, would crumble if the Imperial party and their British allies won the war. Brunet also hoped that with the utter crushing of the Imperial dynasty, maybe in time a republic could eventually blossom in Japan.
By January 1868, Brunet was worried about the issue of the war, as the numerically superior Tokugawa forces were lacking supplies, notably powder and bullets, while Yoshinobu's lack of leadership was sowing doubts among the men. Bedridden due to a mysterious illness, many soldiers believed that their leader was in fact hiding from the fights. Looking at the war map, the Assassin then noted to himself that the fate of Japan would be decided between the little towns of Toba and Fushimi.
After the Battle of Aizu in late 1868, which definitively sealed the fate of the Tokugawa Shogunate, Brunet was invited to drink tea by Harry Parkes, the British Consul. After congratulating the Consul for the victory of his allies, Brunet warned Parkes that "they won a battle, but not the war", with the oblivious Parkes remarked that Britain and France were not at war.
Behind the scenes
In Assassin's Creed: Fragments – The Blade of Aizu, Brunet claimed to be part of the French Third Republic however given the novel's setting of 1868 that should have been the Second French Empire which didn't collapse until 1870.