The brilliant Tokyo chef, who famously sent an eel for a CT scan to better understand its anatomy, is an international sensation. Writer Min Jin Lee has a revelatory meal.

Six days a week, my parents sold Mexican silver earrings to street peddlers for $1.50 at their cramped wholesale jewelry store in Manhattan. Every night, my mother rushed home to Queens to fix delicious Korean suppers from the meat and produce on sale at the Elmhurst Key Food supermarket. Then, in 1981, about five years after we immigrated, my father decided that knowing how to butter bread properly should be as much a part of his children’s education as algebra and spelling. He allowed me, a precocious 12-year-old, to select one fancy restaurant to study each year. On the appointed day, the Lee family would waltz into the likes of Lutèce or Le Cirque.

Our means were modest, but Dad told my two sisters and me to get whatever we fancied. “Does money die or does Lee die?” he’d say. We’d assure him of his immortality, then order beef bourguignon or sole meunière.

I continued these explorations through college and law school, and into my new career as a novelist. Last summer, when my husband, Christopher, and I moved to Tokyo, we ate out frequently. Yet nearly a year after our arrival, we still hadn’t experienced kaiseki, the most traditional—and expensive—style of Japanese cuisine. Kaiseki is an art form: The multicourse banquet incorporates only seasonal ingredients, and the aesthetics of the plate are an important part of the ritual. When I asked native Japanese about the city’s best kaiseki, most had no interest in discussing the subject. They associated it with lengthy, sake-soaked business meals or dismissed it as culinary tourism for Westerners.

But then I heard about the Tokyo restaurant Nihonryori Ryugin, where 38-year-old chef-owner Seiji Yamamoto has ingeniously merged the sacrosanct traditions of kaiseki with futuristic molecular gastronomy techniques (though he doesn’t approve of either label) to international acclaim. Last year, he was invited to give a demonstration at Madrid Fusión, the annual culinary conference where the world’s most brilliant chefs gather to share favorite techniques and ideas. Yamamoto wowed the audience by silk-screening squid ink so that it looked like a page of newsprint. Since then, star chefs such as Joël Robuchon and Ferran Adrià have made pilgrimages to Tokyo to eat at Ryugin. “He is a marvelous guy,” Adrià says, “one of the most important chefs in Japan.” Wylie Dufresne of WD-50 in New York City was amazed by Yamamoto’s demo at another Spanish conference, Lo Mejor de la Gastronomía: “He chopped the head off a live fish and ran what looked like piano wire down its back, which made it go limp.” The technique seemed to prevent the fish from stiffening with rigor mortis, which changes the texture of the flesh.

Yamamoto started cooking as a boy to impress his mother and, after culinary school, spent 11 years training at Aoyagi, a kaiseki restaurant owned by master chef Hirohisa Koyama. In 2003, he opened Ryugin, naming it after a Zen poem describing the strength of a powerful dragon. Although many Western chefs revere Yamamoto, Ryugin generates only modest buzz in Tokyo, which is usually feverish about food trends. While other chefs who trained with Koyama—Hiroyuki Kanda of Kanda and Toru Okuda of Koju—each received three Michelin stars, Yamamoto received two. For me, this meant it was still possible to get a reservation.

When I walked into Ryugin, the doorway was strikingly lacquered with cinnabar. Inside, the whitewashed room was small and modest, with space for just 18 seats in the main area. On the night Christopher and I went, it was filled with Westerners, South Asians and Hong Kong natives—plus one Japanese couple.

We were faced with three set menus in ascending prices and number of courses: Tasting, Gastronomy A and Gastronomy B. In adherence to our we-want-to-see-and-try-everything-so-yes-please temperaments, we selected Gastronomy B—13 courses, the full monty, at $260 a person.

Almost immediately, the sommelier, Takeo Arimasa, placed two small glasses on the table and uncorked a wine bottle labeled Chateau Ryugin.

“I’m sorry, I don’t drink alcohol,” I said.

Arimasa smiled and poured anyway.

The bottle was full of savory hot broth made from Hamaguri clams, a classic kaiseki dish. The cork was stamped Cuvée 1970—the year of the chef’s birth—a playful joke that set the mood for the meal.

Ryugin’s menu includes some elements of kaiseki, but Yamamoto eschews tradition in many ways. A classic kaiseki menu can vary widely in its number of courses, but at a minimum, the meal is comprised of an appetizer (sakizuke), sashimi (mukozuke), a simmered dish (shiizakana), a grilled dish (yakimono) and a steamed dish (mushimono). Yamamoto did not serve sashimi for the second course. Instead, he deep-fried baby sweetfish and plated them as if they were swimming above wavy lines of vinegar mixed with watermelon juice. The fish were barely two inches long and exceedingly tender. But they lacked the characteristic watermelon flavor of the mature fish, so Yamamoto wittily evoked the taste with the watermelon sauce.

For his signature hamo eel soup, Yamamoto called on state-of-the-art medical technology. Traditionally, Japanese chefs remove the hamo eel’s thousands of fine bones with age-old Kyoto knife techniques, but Yamamoto went one step further: He brought an eel to a hospital for a CT scan to study its anatomy. Now, he’s able to carve eels with such precision that he creates chrysanthemum flowers out of the flesh, which appear to float in a deliciously fragrant stock made from eel bones and matsutake mushrooms.

Like his mentor, Koyama, Yamamoto truly understands how to handle fish. He buys mostly live seafood, so his sashimi—including spiny lobster flown in from Brittany, snapper and tender aori-ika squid topped with beluga caviar—was amazingly fresh. He elevated the fish with wonderful dipping sauces such as powdered konbu (sea kelp), pulverized with a Thermomix—a superfast blender, scale, processor and steamer beloved by molecular gastronomists. The savory powder smelled like curry, and dipping exquisite sashimi into the konbu gave it a salty ocean bite.

The next course was also surprising and elegant—grilled tilefish served on what looked like an exquisite pen-and-ink illustration of a fish, but was actually a luscious miso sauce. I insisted on going into the kitchen to ask how Yamamoto created this dish, which the reserved chef did not appreciate. But here’s what this pushy Korean diner learned: The chef first drizzled hot oil onto the fish skin to make it crispy, then grilled the skewered seafood over slender, hand-selected branches of oak charcoal. And the sauce? He silk-screens it onto the plate with “paint” made from squid ink and red miso. (Yamamoto uses the same technique to create a chocolate dessert with a QR code—like a bar code, but with embedded URLs. Point a cell phone camera at the dish, and you can read more information about it on the screen. Sugoi, as the Japanese would say. Cool.)

My husband, the supertaster, was amazed. But I, anxiety-prone, was worried. We had never eaten so brilliantly. How would the meal end? It was time for the famous -196 Degrees Celsius Candy Apple. With spoons, we tapped what looked like a lady apple, so shiny it could have been a Christmas ornament, and it shattered into shards of candy shell. Inside were two bites of powdered ice cream that tasted like the most delicious apple pie ever. How did Yamamoto do it—with liquid nitrogen? When I later tried to ask, he dodged the question, more chef than talker.

When we’d finished the last morsels of candy apple, Yamamoto came out of the kitchen. He was tall, with the open face of an inquisitive and happy child. He stopped at every table, including ours.

“Thank you for coming to the restaurant. I am honored to cook for you,” he said.

My husband complimented the meal, and I considered dropping a wifely footnote to explain that his understated “very good” was better than a dozen Michelin stars. I couldn’t resist. It was like my father was there, too: “It was delicious and beautiful and sugoi,” I told Yamamoto. “And I learned so much.”

Nihonryori Ryugin,

Min Jin Lee, the author of the novel Free Food for Millionaires, lives in Tokyo with her husband and son.