Sounder minds might have questioned the wisdom of dragging a 15-year-old on an almost three-hour bullet train trip to Osaka, then across town to another 90-minute train ride south into the mountains, and finally to a steep ride on a cable car, all for one night at Eko-in, a Buddhist temple on Mount Koya (Koyasan). A sacred place with more than 100 temples, Koyasan was founded in 816 A.D. And after Tokyo, Roger and I needed old. (photo)

Through the Wakayama prefecture volunteer-guide site that serves Koyasan, my detailed letter of request for someone knowledgeable was answered by a Koyasan aficionado. Kaori Kodama, who's spent 13 years studying and guiding tours there, led us inside the monumental temples of this World Heritage site; we watched in awe as a prayer service unfolded with the power of an opera. After our vegetarian dinner was brought to our temple room on low, lacquered trays, Lincoln ignored the TV in our tokonoma (most traditional Japanese rooms have this special viewing niche), preferring to wrap himself in his futon and watch Ratatouille on the laptop—my favorite image of him. In the morning, we entered the cemetery of Okunoin, a mysterious forest with wandering dark paths of moss-covered memorials. It was, fortunately, the first day of spring, when the annual procession of abbots from all of Koyasan's temples heads up to Lantern Hall, where 20,000 lights hang to commemorate ancestors and to bring good fortune. (photo)

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In Kyoto, our timing continued to be lucky. We arrived on the grounds of the Imperial Palace just as the cherry blossoms burst into bloom—pink and red and white, locals joyously photographing them with their cell phones. (Like everyone else in Japan, we had been tracking the flowering at gojapan.about.com/cs/cherryblossoms.) (photo) In this you-should-have-been-here-yesterday world, we also happened to be in town during the one-day-a-month food and antiques market at Kitano Tenmangu Shrine. We scored old kimonos for $20 each, and for less than that we adopted a brass mascot we named the Fish God.

Just as we had in Tokyo, Roger and I craved stillness the way Lincoln craved stimulation, so we yo-yoed between the two. We wandered the old streets of the Gion neighborhood, searching for pottery in ancient shops, only to be dragged to Teramachi-dori to find the latest Boa CD. We longed for a proper tea ceremony lasting hours; Lincoln preferred his tea cold, in a bottle, from a vending machine. Sometimes we just had to leave him behind playing Mario Kart on his Nintendo DS while we went off to Fushimi Inari Grand Shrine (the thousands of vermilion gates undoubtedly played a role in inspiring Christo's installation in New York's Central Park) (photo). The three of us agreed on spectacular cones of green-tea soft-serve ice cream; Nishiki, the covered food-market street where Linc photographed turnip pickles and dried fish (photo); and a magical arm-in-arm walk through the otherworldly moss garden at Saiho-ji Temple, which looked, he proclaimed, "very Miyazaki." (photo)

The most insightful book I read before the trip was Alex Kerr's Lost Japan, about Japanese cultural traditions. It was Kerr who founded Iori, a company that has restored eight machiya—wooden, two-story, former artisan's shops—and rents them weekly as town houses. Our best move was to rent a machiya. The houses, which vary in size (accommodating from two to 14 people), also vary wildly in price, depending on the season. We averaged about $110 per person. (photo)

Our former teahouse seemed unadorned at first. Slowly, we noticed the details. We counted a dozen woods, ranging from the pale-blond cypress of the soaking tub to the rough-hewn dark-cedar of the beams. Windows have sliding shoji, their surfaces patterned by divided grids and bamboo blinds. Soft futons float on sheer, woven tatami. The low beams threatened our foreheads, and, as I reminded Linc, "They teach humility—you're forced to bow."

The best amenity was the support staff. Bodhi Fishman, Iori's director, has the depth of a scholar and the grace of a born host, pointing us to the best knife maker (Aritsugu) and to a convenience store for cheap breakfast food, turning us on to small neighborhood restaurants (at chef Takashi Tsubaki's Negiya Heikichi, we learned the meaning of oishii, or "delicious"), and setting up a visit to a kimono-making studio (photo), Tomi­hiro Dyeing, where Lincoln was allowed to paint his own swath of fabric. Bodhi even showed us how to manipulate the machiya's washing machines.

Lincoln lobbied for a return to Tokyo, but I wanted us to have the experience, though a splurge, of a night in an authentic ryokan, Monjuso, where dinner and breakfast are served in the room. (Plus, I yearned to visit Iio-Jozo, an artisanal vinegar brewery.) So we climbed on the train again, north to Amanohashidate, on the Sea of Japan. (photo) Nearby Ine is a fishing village that looked just like we wanted it to.

One of the marvelous things about Japan, for our family anyway, was that, indeed, we could all get what we wanted. For Roger and me, that meant temples, gardens, and museums—intrinsically Japanese places whose very ancientness is their charm. Most of what made Lincoln's top 10 list, including the shinkansen (bullet train) we took back to Tokyo, didn't make Roger's or my list. But for Lincoln, Japan wasn't so much a foreign country as a place from his childhood that he knew was there all along.

TOKYO

LODGING
Keio Plaza Hotel Tokyo
2-2-1 Nishi-Shinjuku, Shinjuku-ku, 011-81/3-3344-0111, keioplaza.com, double from $163

FOOD
Ginza Mitsukoshi
4-6-16 Ginza, Chuo-ku, 011-81/3-3562-1111, mitsukoshi.co.jp