The Shinsengumi submitted a letter to the Aizu clan, another powerful group who supported the Tokugawa regime, requesting their permission to police Kyoto. The request was granted.
On September 30, 1865 (lunar calendar August 18), the Chōshū (anti-Tokugawa) clan were forced from the imperial court by the Tokugawa, Aizu and Satsuma clans. The Shinsengumi were sent to aid the Aizu and guard the gates of the imperial court. The new name "Shinsengumi" may have been coined by Matsudaira Katamori (the daimyō of the Aizu clan) around this time. The opposition forces included the Mori clan of the Chōshū and the Shimazu clan of Satsuma.
In 1864, in an incident at the Ikedaya Inn, Kyoto, thirty Shinsengumi suppressed a cell of twenty Choshu revolutionaries, possibly preventing the burning of Kyoto. The incident made the squad more famous and led to soldiers enlisting in the squad.
n 1867, when Tokugawa Yoshinobu withdrew from Kyoto, the Shinsengumi left peacefully under the supervision of the wakadoshiyori, Nagai Naoyuki.(p172–174) The emperor Meiji had been named the head of a new government (meaning the end of over a century of military rule by the shoguns). This marked the beginning of the Boshin civil war.
Following their departure from Kyoto, the Shinsengumi fought in the Battle of Toba-Fushimi.(p177) At Fushimi, Kondo suffered a gunshot wound but went on to fight at the Battle of Kōshū-Katsunuma. He was then captured in Nagareyama. After surrendering to imperial government forces, he was declared guilty of participation in the assassination of Sakamoto Ryōma and was beheaded in Itabashi three weeks later. Kondo was killed near Tokyo.
The Shinsengumi fought in defense of Aizu territory under Saitō Hajime and joined the forces of the Republic of Ezo in the north.(p217–230) Shinsengumi numbers grew to over one hundred in this period and they fought on despite the fall of Edo and clear defeat of Tokugawa. For example, Hijikata led a daring but doomed raid to steal the imperial warship, the Kotetsu. Hijikata's death from a gunshot wound on June 20 (lunar calendar May 11), 1869, in Hokkaido, marked the end of the Shinsengumi. Before his death, he wrote of his loyalty to the Tokugawa
"Though my body may decay on the Island of Ezo,
My spirit guards my lords in the East."
 Even so, another group of survivors, under Sōma Kazue, who had been under Nagai Naoyuki's supervision at Benten Daiba, surrendered separately,(p246) and a few core members, such as Nagakura Shinpachi, Saitō Hajime, and Shimada Kai, survived the war. Some members, such as Takagi Teisaku, went on to become prominent figures.
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. Retrieved 2016-06-24.