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The Second Choshu expedition was a punitive expedition led by the Tokugawa Shogunate against the pro-Imperial Choshu Domain in 1866.

Following the pro-Shogunate cause's bloodless victory in the 1864 First Choshu expedition, the ruling moderate Zokuronto ("Vulgar View Party") party in Choshu faced a rebellion from pro-Imperial factions of the Kiheitai, prompting the downfall of the party and prompting another Shogunal expedition against the Domain. By January 1865, Shogunal forces withdrew from the domain after the Zokuronto presented goodwill towards the bakufu, but they faced a challenge in disbanding the scattered Kiheitai, who had various units working autonomously from one another. On 13 January 1865, Takasugi Shinsaku, Yamagata Aritomo, and Ito Hirobumi led a rebellion in Shimonoseki, defeating the moderate government's army. By 12 March 1865, the rebel army reigned supreme in Choshu and called for the reinstatement of the Mori clan. In Osaka, the Shogun arrived to deal with the punishment for the Mori clan. Before the news of the rebellion reached Osaka, the Shimazu Domain persuaded the Shogun to give a lenient punishment to the Choshu daimyo Mori Yoshinaka, allowing him to abdicate in favor of his grandson and reduce the size of his domain. When the news of the punishment arrived at the Choshu capital of Hagi, however, Kido Koin and other extremist samurai rejected it. Kyoto then sanctioned another expedition against Choshu on May 1865.

Preparations fro the expedition lasted about a year, and Matsudaira Katamori and Osagawara Nagamichi set up three fronts against Choshu: Aki Province in the southeast, Iwami Province in the northeast, and Buzen Province to the southwest. The Satsuma Domain and other tozama (anti-Tokugawa) daimyos like the Tosa Domain refused to support the expedition or send contingents for the expeditionary force. In July 1866, the Tokugawa coalition began its attack from Hiroshima.The sampeitai captured the island of Oshima on 12 July 1866, but Shogunal forces advancing in Aki were ambushed and defeated by Choshu forces on 26 July. At the same time, Inoue Bunta and Omura Masujiro's Choshu forces defeated bakufu forces in mainland Iwami. Before July ended, Choshu warships attacked bakufu positions in Buzen, and Choshu samurai also mounted an amphibious attack that defeated the Tokugawa troops. On 29 July, French warships en route to Nagasaki arrived in Shimonoseki and threatened the Choshu with military action if they did not surrender to the bakufu. However, the French warships eventually left when their British rivals arrived, and the fighting continued. On 5 August 1866, both sides suffered heavy losses at Shijuhasaka, and, in September, bakufu forces retreated from Buzen as Choshu forces advanced. On 16 September, Ono fell to the Choshu and the bakufu army retreated back to Hiroshima. The death of Shogun Tokugawa Iemochi led to Matsudaira Katamori and Hitotsubashi Keiei using the mourning as a pretense for a ceasefire. By then, rumors of a "Satcho Alliance" between Satsuma and Choshu, and supported by the British, had already spread.

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