Japan: From the Samurai to the Atomic Age

You travel to Kyoto on the Haruka Express, about an hour and a quarter, and check in, then begin where the old order ended. Nijō-jo Castle was built as the Kyoto seat of the Tokugawa shoguns, a fortified palace of moats, painted screens and “nightingale” floors engineered to squeak underfoot and betray an assassin. It was in the great hall of the Ninomaru Palace, in the autumn of 1867, that Tokugawa Yoshinobu, the fifteenth and last shogun, born in 1837 and alive until 1913, assembled the lords of the realm and returned governing authority to the Emperor. The building where he did it is still standing, and you will walk through it.

The afternoon moves from the political to the material. The Museum of Kyoto occupies the former Bank of Japan Kyoto branch, a Meiji-era brick building from 1906 that is itself an artifact of the Westernization program, and covers the city’s history from the imperial court to the modern era. At the Samurai Ninja Museum you view authentic period armor and then wear a full replica suit, with optional tea ceremony and shuriken throwing indoors. You close the day at Jōnangū Shrine, whose gardens are laid out in the Heian court style that the Restoration took as its model for what it was restoring, and which stands on the Toba-Fushimi battlefield. Here, in January 1868, an outnumbered imperial army carrying modern rifles broke a larger shogunate force and turned a political crisis into the Boshin War. This is the ground the fall of the samurai actually happened on.

The tour is called a restoration for a reason, and today is about what was being restored. Heian Jingū was built in 1895 to mark eleven centuries since Kyoto was founded as the imperial capital, and it enshrines the first emperor to rule from the city and Emperor Kōmei, the last emperor of the old order, who died in 1867 on the eve of everything. Its torii is one of the largest in Japan and its garden is among the finest surviving Meiji-era landscapes.

At the Kyoto Handicraft Center you have a 45-minute meet-and-greet with a maiko, an apprentice geiko, including a photo session, a rare chance to ask questions of someone inside a tradition that predates the Restoration and survived it. You continue to Kōdai-ji Temple, founded in 1606 by the widow of Toyotomi Hideyoshi, with its bamboo grove and its hillside gardens above the Higashiyama district. If time permits, the day ends at Fushimi Inari Shrine, where thousands of vermilion torii gates, each one donated by a business or family, climb the mountain in an unbroken tunnel.

The Restoration was made by young men from the outer domains, most of them low-ranking samurai, many of them killed before they saw it finished. The Ryōzen Museum of History is devoted to them: it specializes in the Meiji Restoration and the figures who drove it, and its collection includes the revolver carried by Sakamoto Ryōma, the Tosa samurai who brokered the alliance between the rival domains of Satsuma and Chōshū that made the overthrow of the shogunate possible, and who was assassinated in Kyoto in 1867 at the age of thirty-one.

From the museum you go to the pistol’s most famous moment. At the Teradaya Inn in Fushimi, in 1866, shogunate agents surrounded Ryōma in his lodgings and he fought his way out with a Smith & Wesson revolver, wounded in the hands, warned in time by a woman who ran up the stairs from the bath. The building is preserved as a museum. The day closes at Kiyomizu-dera, the great temple on the eastern hills, where the Otowa waterfall splits into three streams for health, love and success, and where the view over Kyoto is the one every visitor to this city has carried away for four hundred years.

You travel by train from Kyoto Station to Itami Airport, fly to Nagasaki, and transfer about forty-five minutes by coach into the city. Nagasaki is why this tour is possible: the one harbor the Tokugawa never closed completely, and therefore the seam through which everything foreign entered Japan: guns, ships, medicine, Christianity, coal technology and revolution.

The afternoon is at Glover Garden, the hilltop estate of Thomas Blake Glover, a Scottish merchant who arrived in 1859 at twenty-one and reshaped the country. He introduced Japan’s first steam locomotive, brought in modern coal mining at Takashima, founded the Kosuge slip dock and shipyard that grew into Mitsubishi Heavy Industries, and started the brewery that became Kirin. He also ran rifles and warships to the anti-shogunate domains of Satsuma and Chōshū in defiance of British treaty obligations and Japanese law, arming the men who would win the Boshin War and form the Meiji government. His house, Japan’s oldest surviving Western-style building, looks out over Nagasaki Bay. Next door stands Ōura Cathedral, built in 1864, the oldest surviving church in Japan, a designated National Treasure and part of the UNESCO World Heritage listing for Hidden Christian Sites. This is the place where, months after it opened, a group of villagers quietly identified themselves to a French priest as the descendants of Catholics who had kept the faith in secret for seven generations.

At two minutes past eleven on the morning of August 9, 1945, a plutonium implosion bomb detonated roughly five hundred meters above the Urakami valley, over the largest Catholic community in Japan and a city that had been the country’s window on the West for three hundred years. You will spend the morning at the Nagasaki Atomic Bomb Museum, Nagasaki Peace Park and the hypocenter. Your historian will speak here. This is a difficult stop and it is not optional to understanding the rest of the tour.

The afternoon returns to the century that led here. The Nagasaki Museum of History and Culture is a world-class collection of samurai culture and armor, of Nagasaki’s role as the point of contact with the outside world, and of the Restoration itself, including displays of the Western and Japanese weapons actually used in the Boshin War. Seeing those rifles a few hours after standing at the hypocenter is the entire argument of this tour compressed into a single day: eighty years separate them.

You begin at the Tateyama Air Raid Shelter Complex, a set of concrete tunnels cut into the hillside that served as the Nagasaki prefectural defense headquarters. Officials were inside it when the bomb went off, and their accounts of that moment are displayed where they were written. Above it lies Tateyama Park, on high ground with a long view back down over the harbour and the Urakami valley, which gives you the geography of the following morning’s stops before you make them.

The rest of the day is the long story of Japanese isolation and the people it was enforced against. Dejima is the fan-shaped artificial island in Nagasaki harbor where Dutch traders were confined from 1641 until the country reopened, restored now as a living history museum of warehouses, offices and residences; for two hundred years, this was Japan’s only authorized channel to Europe. At Kazagashira Park you find the statue of Sakamoto Ryōma looking out over the harbor, and the restored headquarters of Kameyama Shachu, the trading company Ryōma founded here, in effect Japan’s first modern corporation, to move Glover’s rifles to the domains that would use them against the shogun. You finish on Nishizaka Hill, a short walk from Nagasaki Station, at the Monument and Museum of the 26 Martyrs: six foreign missionaries and twenty Japanese Catholics, the youngest twelve years old, arrested in Kyoto and Osaka, marched some six hundred miles in winter, and crucified here in February 1597. The monument has been visited by two popes, John Paul II in 1981 and Francis in 2019.

You transfer to Nagasaki airport and fly to Haneda, an hour and forty minutes, arriving in the capital the Restoration created. When the emperor left Kyoto in 1868 and moved into the shogun’s castle in Edo, the city was renamed the Eastern Capital and the whole center of gravity of the country shifted with him.

You will visit the Imperial Palace and East Gardens, built on the foundations of Edo Castle, the Tokugawa seat of power for two and a half centuries, and view the Nijūbashi, the double bridge that is the palace’s public face. In the plaza outside stands the equestrian statue of Kusunoki Masashige, the fourteenth-century commander who fought and died for an emperor against overwhelming odds. He was a minor medieval figure until the Meiji state made him the model of loyalty for a modern nation, and by the 1940s every Japanese soldier knew his name. Standing in front of it, you can see exactly how a government builds a myth it will later need.

Yasukuni Shrine was founded in 1869, on the emperor’s order, to enshrine the spirits of those who died fighting for the imperial cause in the Boshin War. Over the following century its lists grew to include the dead of every war Japan fought, and the question of who belongs on them has made it one of the most contested sites in East Asia. On the grounds stands the Yūshūkan, Japan’s oldest military museum, which presents the country’s wars in terms many foreign visitors find difficult and some find indefensible. You will tour it with a historian who reads Japanese, who has spent decades interviewing Japanese veterans, and who will tell you plainly what the exhibits say, what they leave out, and why the argument matters. Lunch is at the museum.

The afternoon is free for packing, for Tokyo, or for whatever you have been meaning to see. The group gathers in the evening for a farewell dinner to close out the journey: ten days, four cities, and the span from a warrior class that had ruled since 1603 to the morning the war ended.

One morning transfer from the hotel to Narita International Airport (NRT) for flights home. Allow roughly ninety minutes for the drive, plus international check-in.