By the autumn of 1868, the Tokugawa shogunate (徳川幕府, Tokugawa bakufu) had ceased to exist as a political entity. The Battle of Toba-Fushimi (鳥羽・伏見の戦い, Toba-Fushimi no Tatakai) in January of that year had shattered its military dominance; domain after domain had submitted to the new Meiji government. But Enomoto Takeaki (榎本武揚, Enomoto Takeaki), a 32-year-old former Tokugawa naval commander who had studied in the Netherlands and understood Western military systems as well as anyone in Japan, refused to accept the outcome. In August 1868, he slipped out of Edo (江戸, Edo) harbor with eight warships — the bulk of the shogunate's surviving naval force — declining to hand them over to the imperial government as ordered.

He sailed north. There was almost nowhere left to go. Chasing his options to the end of the map, Enomoto landed in Hokkaido (北海道, Hokkaidō) — then called Ezo (蝦夷), the frontier island — in late 1868. With approximately 3,000 men, mostly former shogunate soldiers and officials who had nowhere else to go, he took control of Hakodate (函館, Hakodate) and its remarkable fortress. Goryokaku (五稜郭, Goryōkaku) was a star-shaped Western-style fort built by the shogunate in 1866, designed by Dutch-trained engineer Takeda Ayasaburo (武田斐三郎, Takeda Ayasaburō) using European star-fort principles. The five angular bastions were arranged to eliminate blind spots in cannon coverage — the fortress built to repel Western warships was now the last headquarters of the men who had lost to the Meiji emperor.

The officers of the new republic held an election to choose their leader. Enomoto won a majority of votes and was named sosai (総裁, sōsai) — president. On December 15, 1868, the Republic of Ezo (蝦夷共和国, Ezo Kyōwakoku) was formally proclaimed. It may be the only democratic election in the entire history of the samurai class. The republic set up a functioning government, issued its own policies, and prepared its defenses. It controlled the northern island. It had a navy. For roughly six months, it was a real, operating state.

Imperial forces under Kuroda Kiyotaka (黒田清隆, Kuroda Kiyotaka), numbering approximately 7,000 men, landed near Hakodate in April 1869 and began the final siege. The republic's defenders fought back. Among the most committed was Hijikata Toshizo (土方歳三, Hijikata Toshizō), the former vice-commander of the Shinsengumi (新選組, Shinsengumi) — the shogunate's elite police force, feared for its iron discipline, and of which Hijikata had been the strict and merciless enforcer, earning the nickname "Demon Vice-Commander." He had survived the collapse of the shogunate and found a last purpose in Hokkaido. In his final days, accounts suggest he wore a Western-style military uniform rather than samurai dress. On June 20, 1869, Hijikata died by rifle fire during a cavalry charge near Ippongi Kanmon (一本木関門, Ippongi Kanmon). He was 34 years old. A samurai, in Western clothes, charging into rifle fire, at the very end of the samurai age.

Seven days after Hijikata's death, on June 27, 1869, Enomoto Takeaki surrendered to Kuroda Kiyotaka. He emerged from Goryokaku and accepted capture, reportedly weeping. He asked that his men be spared; he offered his own life in their place. The Meiji government accepted neither offer in full — most of his followers were pardoned almost immediately, while Enomoto was imprisoned. But Kuroda, the general who had just defeated him, became one of the loudest voices arguing for Enomoto's release. The request for clemency came from the man who had accepted the surrender.

In 1872, Enomoto was pardoned. What followed was one of the most remarkable reversals in Japanese history. The man who had refused to surrender the shogunate's navy, who had built a rebel republic in the northern wilderness and held it for six months against imperial forces, went on to serve the Meiji state he had fought against: Navy Minister (1880), Minister of Communications (1885 to 1888), Minister of Education, and Foreign Minister. Five cabinet posts in the government of the Japan he had tried to prevent. During the siege, he had sent the Meiji government a rare Dutch maritime law book he was carrying, saying it was too valuable to be destroyed in battle. Officials who received the gesture never forgot it.

With the surrender at Goryokaku, the Boshin War was over and the Meiji government for the first time held authority over the entire Japanese archipelago. The fortress itself eventually became a public park — its star shape, visible from the air, became one of Hokkaido's most recognizable landmarks. The men who refused to accept the end of the old world had, in their defeat, helped build the new one.