The Bakufu during its last years—bakumatsu—has taken strong measures to try to reassert its dominance, although its involvement with modernization and foreign powers has made it a target of anti-Western sentiment throughout the country.

Naval students have been sent to study in Western naval schools for several years, starting a tradition of foreign-educated future leaders, such as Admiral Enomoto.

The French naval engineer Léonce Verny had been hired to build naval arsenals, such as those at Yokosuka and Nagasaki.

By the end of the Tokugawa shogunate in 1868, the Japanese navy of the shogun will already possess eight western-style steam warships around the flagship Kaiyō Maru, which will be used against pro-imperial forces during the Boshin war, under the command of Admiral Enomoto.

A French Military Mission to Japan (1867) is established to help modernize the armies of the Bakufu.

Japan sends a delegation to and participates in the 1867 World Fair in Paris.

Tokugawa Yoshinobu (also known as Keiki) had reluctantly became head of the Tokugawa house and shogun following the unexpected death of Tokugawa Iemochi in mid-1866.

Tokugawa Yoshinobu tries to reorganize the government under the Emperor while preserving the shogun's leadership role, a system known as kōbu gattai.

Fearing the growing power of the Satsuma and Chōshū daimyos, other daimyo call for returning the shogun's political power to the emperor and a council of daimyos chaired by the former Tokugawa shogun.

On November 9, 1867, a secret order is created by Satsuma and Chōshū in the name of Emperor Meiji commanding the "slaughtering of the traitorous subject Yoshinobu."

Just prior to this however, and following a proposal from the daimyo of Tosa, Yoshinobu resigns his post and authorities to the emperor, agreeing to "be the instrument for carrying out" imperial orders.

The Tokugawa Shogunate has ended.

Enomoto Takeaki, vice-commander of the Shogunate Navy, had refused to remit his fleet to the new government and had departed Shinagawa on August 20, with four steam warships (Kaiyō, Kaiten, Banryū, Chiyodagata) and four steam transports (Kanrin Maru, Mikaho, Shinsoku, Chōgei) as well as two thousand sailors, thirty-six members of the "Yugekitai" (guerilla corps) headed by Iba Hachiro, several officials of the former Bakufu government including the vice-commander in chief of the Shogunate Army Matsudaira Taro, Nakajima Saburozuke, and members of the French Military Mission to Japan, headed by Jules Brunet.

On August 21, the fleet had encountered a typhoon off Choshi, in which Mikaho was lost and Kanrin Maru, heavily damaged, had been forced to rally the coast, where she was captured at Shimizu.

The rest of the fleet had reached Sendai harbor on August 26, one of the centers of the Northern Coalition against the new government, composed of the fiefs of Sendai, Yonozawa, Aizu, Shōnai and Nagaoka.

Imperial troops have continued to progress north, taking the castle of Wakamatsu, and making the position in Sendai untenable.

On October 12, 1868, the fleet leaves Sendai, after having acquired two more ships (Oe and the Hou-Ou, previously borrowed by Sendai domain from the Shogunate), and about a thousand more troops: former-Bakufu troops under Otori Keisuke, Shinsengumi troops under Hijikata Toshizo, Yugekitai under Katsutaro Hitomi, as well as several more French advisors (Fortant, Marlin, Bouffier, Garde), who had reached Sendai overland.

The rebels, numbering around three thousand and traveling by ship with Enomoto Takeaki, reach Hokkaidō in October 1868.

They land on Takanoki Bay, behind Hakodate on October 20.

Hijikata Toshizo and Otori Keisuke each lead a column in the direction of Hakodate.

They eliminate local resistance by the forces of Matsumae domain, which had declared its loyalty to the new Meiji government, and occupy the fortress of Goryokaku on October 26, which becomes the command center for the rebel army.

The rebels, after eliminating all local resistance, establish the Ezo Republic on December 25, with a government organization modeled after that of the United States, with Enomoto Takeaki, as President.

While the governments of France and the United Kingdom conditionally recognize the new republic, the Meiji government in Tokyo does not.

The independent Japanese "Republic of Ezo" is proclaimed on January 27, 1869 (New Style), with a government organization based on that of the United States, with Admiral Enomoto Takeaki elected as its first president (sosai).

Elections are based on universal suffrage among the samurai class.

This is the first election ever held in Japan, where a feudal structure under an Emperor with military warlords is the norm.

Through Hakodate Magistrate Nagai Naoyuki, attempts are made to reach out to foreign legations present in Hakodate to obtain international diplomatic recognition.

The treasury includes one hundred and eighty thousand gold ryō coins Enomoto had retrieved from Osaka Castle following Shōgun Tokugawa Yoshinobu's precipitous departure after the Battle of Toba–Fushimi in early 1868.

After the defeat of the forces of the Tokugawa shogunate in the Boshin War (1869) of the Meiji Restoration, a part of the former shōgun's navy led by Enomoto had fled to the northern island of Ezo (now known as Hokkaido), together with several thousand soldiers and a handful of French military advisers and their leader, Jules Brunet.

Enomoto makes a last effort to petition the Imperial Court to be allowed to develop Hokkaido and maintain the traditions of the samurai unmolested, but his request is denied.

A defense network had been established around Hakodate during the winter of 1868–1869 in anticipation of the attack by the troops of the new Imperial government.

The defenses around the southern peninsula of Hakodate have been enhanced, with the star fortress of Goryōkaku at the center.

The Ezo Republic troops are structured under a hybrid Franco-Japanese leadership, with Commander in chief Otori Keisuke seconded by Jules Brunet, and each of the four brigades commanded by a French officer (Fortant, Marlin, Cazeneuve, Bouffier), seconded by eight half-brigade Japanese commanders.

Two ex-French Navy officers, Eugène Collache and Henri Nicol, have further joined the rebels, and Collache has been put in charge of building fortified defenses along the volcanic mountains around Hakodate, while Nicol is in charge of reorganizing the Navy.

The Bakufu is abolished following the Boshin war (1868–1869), and Keiki is reduced to the ranks of the common daimyo.

Japan's first major naval engagement between two modern navies, the Naval Battle of Hakodate Bay, occurs towards the end of the Boihin War, during the month of May 1869.

Before the final surrender, in May 1869, the Ezo Republic French military advisors escape to a French Navy warship stationed in Hakodate Bay, the Coëtlogon, whence they return to Yokohama and thence to France.

After having lost close to half their numbers and most of their ships, the military of the Ezo Republic surrenders to the Meiji government on May 17, 1869.

The battle marks the end of the old feudal regime in Japan, and the end of armed resistance to the Meiji restoration.

After a few years in prison, several of the leaders of the rebellion will be rehabilitated, and will continue with brilliant political careers in the new unified Japan: Enomoto Takeaki in particular will assume various ministry functions during the Meiji era.