Shortly after the arrival of the Perry Expedition challenging Japan national isolation policy, Nagai was appointed as a metsuke and was placed in charge of casting new cannons for coastal defense.

In 1855, Nagai was transferred to the newly formed Nagasaki Naval Training Center, where he served as its director, overseeing a group of Dutch military advisors and students from various domains around Japan in studies of western warship technologies.

In 1857, with the opening of the Tsukiji Naval Training Center, Nagai returned to Edo on board the Kankō Maru, Japan's first steam warship, together with 103 of his students.

The city was filled with numerous rōnin, many of whom supported the sonnō jōi movement and who did not hesitate to use assassination or terrorist tactics to further their political agenda.

[4] Returning to Edo following the Battle of Toba–Fushimi, Nagai joined Enomoto Takeaki and the remnants of the Tokugawa navy, boarding the Kaiten and heading to Ezo by way of Matsushima, in Sendai Domain.

However, the Imperial Army soon began its attack on Hokkaido, and Nagai surrendered at the small fortress of Benten Daiba, along with the survivors of the Shinsengumi.

After a period of three years in prison, he was pardoned by the Meiji government in January 1871, and again rose to positions of political prominence, serving most notably as the secretary to the Genrōin from July 1875 to October 1876.