A 21-day Japan itinerary

It is not just Shibuya and Asakusa. Tokyo is the stone base of Edo Castle, once the largest in the world, sitting in a free public garden; it is Toyosu, the biggest fish market on earth, with glazed walkways above the tuna auction and sushi counters serving from first light; it is kabuki at the Kabukiza with single-act tickets sold same-day at the side window, no booking; and it is the whole forest wrapped around Meiji Jingu, minutes from Harajuku.

Half the dishes in a modern Japanese cafe were invented here: spaghetti napolitan, doria and iekei ramen all came out of places still open today. That is what a port opened to foreigners leaves behind: a Chinatown that is not a restaurant strip but a neighbourhood with its own schools and working temples, seven Western houses on the Yamate bluff that cost nothing to visit, and a cruise terminal without a single step whose timber deck is a public park.

The city where you watch Japan being manufactured: the Toyota museum traces the jump from the loom to the car with the machines running, and an hour away you can look down from a walkway onto a real assembly line, kanban cards moving along it. The castle has rebuilt its residential palace in cypress with traditional joinery — you go in barefoot — and you eat hitsumabushi, grilled eel served three different ways in the one bowl.

The old capital holds a density no other Japanese city matches: the garden at Tenryu-ji is the only one in Kyoto that keeps the layout Muso Soseki gave it in the fourteenth century, To-ji's Kodo holds twenty-one sculptures arranged as a mandala in three dimensions, and the Imperial Palace is now simply walked into, no application and no ticket, while Katsura Rikyu has to be applied for months ahead. Then there is the torii forest of Fushimi Inari, the gold leaf of Kinkaku-ji and the sand sea of Ginkaku-ji.

Day trip to Nara

This city eats standing up and out loud: the neon of Dotonbori over the canal, takoyaki, okonomiyaki and kushikatsu, the izakaya alleys of Ura-Namba and, around Tenma station, the densest cluster of stand-up bars in Japan. Kitsune udon was invented here, and Osaka was pressing sushi in wooden boxes before Tokyo got round to nigiri. It is also home to Taro Okamoto's Tower of the Sun, seventy metres of sculpture you walk inside.

Day trip to Himeji · Kobe

Home to Korakuen, one of Japan's three great landscape gardens, and to the black "crow castle", with the Kibi Plain and its shrines and burial mounds half an hour away by bicycle. It is also the rail hub that opens up Kurashiki, the Inland Sea islands and Shikoku.

Day trip to Takamatsu

Tanabe is where you start walking the Kumano Kodo, the network of pilgrimage trails crossing the forested mountains of the Kii peninsula and twinned with the Camino de Santiago: anyone who has walked sections of both registers here as a Dual Pilgrim. Along the way is Yunomine, one of the oldest hot springs in Japan, with a wooden hut for two set in the stream whose water changes colour several times a day.

The first island Izanagi and Izanami create in Japan's founding myth, home to the shrine tradition calls the country's oldest and to three Tadao Ando buildings within half an hour of each other. And, on the same island, the park with a life-size Godzilla and a Hidden Leaf Village built in the woods.

The castle town that produced both the Iga school of ninjutsu and the poet Basho: a farmhouse with genuine booby traps and an archive of real ninja documents, a 30-metre castle wall topped by a wooden keep one local man paid for in 1935, and all around it a basin of rice paddies, pottery kilns and Iga beef cattle.

One of Japan's great hidden Buddhas: a seated bronze statue 17 metres tall, the largest indoor Buddha in the country, inside Seidai-ji Temple, with a five-story pagoda reached by elevator and a stone garden recreating the Nine-Dragon Wall.

The thatched roofs are rebuilt whole every thirty or forty years in a single day, with the entire village up on the frame: that custom, the yui, is what has kept standing the gassho-zukuri houses you look down on from the Ogimachi hill. Once the coaches leave the hamlet falls silent, and what is left is a handful of beds in family homes, dinner round the hearth, and doburoku, a cloudy sake that by a legal exception may only be brewed here.

Whole streets of Edo-period wooden houses with century-old sake breweries open for tasting, and a morning market along the Miyagawa where the growers set up their own stalls. Hida's carpenters were already working for the imperial court in the eighth century, and the town is still the centre of Japanese furniture-making. The float festival happens twice a year, spring and autumn; in winter hoba miso is grilled on a dried magnolia leaf.

Iida, a quiet city in southern Nagano known for its apples and Tenryu River cruises, serves as the gateway to Magome, the Nakasendo post town where the road's most famous walk begins: 8km of forest and farmland to neighbouring Tsumago.

Day trip to Narai-juku

Saitama's mountain basin, ninety minutes from Ikebukuro and still almost untouched by foreign tourism: a valley closed in by peaks, with terraced rice paddies, a 34-temple Kannon pilgrimage threading through the hamlets, the Nagatoro gorge, and December's Yomatsuri - one of Japan's three great float festivals and the only one that sets off fireworks in midwinter.

Fukuroda Falls, 120m spread across four tiers (nicknamed the 'waterfall of the four seasons' for how radically it changes look through the year), together with the smaller Namase and Tsukimachi falls, linked by a full-day hiking trail of about 5 hours; the town also has three distinct types of hot spring (Daigo, Fukuroda, and Tsukiore) and, nearby but reached from a different station (bus ~40min from Hitachiota), the Ryujin Suspension Bridge, home to Japan's highest bungee jump.

The best-preserved samurai quarter in northern Japan: wide earth streets between black wooden fences, with warrior-family houses you can go inside. Four hundred weeping cherries bloom over them in late April, and in winter those same fences under snow are the other reason to come. Fifteen minutes by train from the deepest lake in Japan and from the seven hot-spring inns hidden in the forest of Nyuto.

A hot spring town along the Kinugawa River gorge, with traditional ryokan perched over the canyon, the Tobu World Square theme park (1:25-scale miniature replicas of world monuments, from the Parthenon to Tokyo Tower), walks and boat rides along the gorge itself, and, further up the valley, the gateway to even more remote hot springs like Yunishigawa and Okukinu.

The mausoleum of Tokugawa Ieyasu is gilded carving from top to bottom, with the three monkeys relief and the Yomeimon gate, reached along a thirty-seven-kilometre avenue of cryptomeria planted in the seventeenth century. Past Kegon falls lie Lake Chuzenji and the Senjogahara marsh, with bears and boardwalks; in summer Nantai is climbed as a pilgrimage, and in winter the Unryu canyon fills with columns of ice.

A 1,200-year-old hot spring village that also happens to be a ski resort: thirteen public bathhouses run by the residents themselves, water surfacing at 90°C in the middle of the lanes, 1,085 metres of powder-covered vertical above the rooftops, and, every 15 January, one of Japan's three great fire festivals.

Day trip to Jigokudani / Shibu Onsen

The valley that hosted the 1998 Olympic downhill: ten ski resorts beneath a wall of 3,000-metre peaks, around ten metres of snow a season, and in summer the Daisekkei snow gorge and the Tsugaike wetlands.

Six linked modes of transport — funicular, highland bus, tunnel electric bus, a ropeway with no pylons, an underground cable car and one more bus — carry you across the Japanese Alps from Toyama to Nagano via Murodo at 2,450 m, with the spring snow corridor at one end and the Kurobe Dam at the other. It only operates from mid-April to the end of November.

A mountain retreat for summer visitors since the Meiji era, with Shiraito Falls, the century-old shops of Kyu-Karuizawa Ginza street, and one of Japan's largest outlet malls right by the station.

The Fuji Five Lakes area, with the mountain's most iconic views: Lake Kawaguchiko, Chureito Pagoda rising above Mt. Fuji, the pond village of Oshino Hakkai, and ryokan with hot springs facing the mountain directly.

Hakone is not a spa town but a forty-square-kilometre caldera with a dome in the middle: seven historic springs, each with its own chemistry and temperature, which is why the afternoon in the ryokan's rotenburo is the plan and not the trimming. You come up on Japan's oldest adhesion mountain railway, with three switchbacks, and cross Lake Ashi by boat. June brings hydrangeas along the embankment; October, the golden susuki of Sengokuhara.