One of the best things about travel is that it seems perfectly OK, away from home, to eat dessert for breakfast. Our Sunday morning begins at Sadaharu Aoki, the namesake, gleaming-white Ginza shop of a talented young pastry chef. Pastry is one of Tokyo's current fixations, with cutthroat competition to create French confections that outdo their Parisian twins (pitch-perfect madeleines and éclairs), or to put new spins on classic wagashi (Japanese sweets). Aoki is one of the city's up-and-coming pastry wizards, and I'm especially taken with his matcha éclairs, striking for their green icing (made with natural matcha green-tea powder) on an otherwise impeccable, classic cream-filled choux pastry.

When it comes to cloning—be it French pastries or American and European restaurants and fads—no one touches the Japanese. Foreign foods and fashions get duplicated so faithfully here that the originals start to look like tired, lazy copies. But how do they deal with foreigners who have the nerve not just to clone Japan's most cherished, obsessed-over dishes, but to do it right here in Tokyo? To find out, we head for lunch in the Setagaya district, where New York–born Ivan Orkin—a Culinary Institute of America graduate who worked at Lutèce and Mesa Grill in Manhattan and has lived in Japan off and on since the late 1980s—opened Ivan Ramen last summer. We find a long line outside the tiny 10-seat shop, and we queue up along with nearly two dozen Japanese ramen buffs (known as ramen otaku, or "ramen geeks"). Orkin, a lifelong ramen otaku, makes his own noodles, a rare thing even at Japan's most hard-core ramen shops. I order shoyu (soy sauce) ramen with pork, and he hands me a bowl of freshly made noodles topped with juicy braised pork, an egg and nori in a soy-seasoned broth made from chicken and seafood. Compared with the ramen I've had in established, Japanese-run Tokyo spots like Kyushu Jangara—which specializes in Kyushu island's creamy, pork-based tonkotsu broth—Orkin's noodles easily hold up. The other guests seem just as transfixed, slurping their ramen and snapping photos of it.

Sunday afternoon is Harajuku time: Takeshita-Dori street in the Harajuku area is where teens, dressed to out-shock each other, congregate on Sundays to stroll, show off and shop in the inexpensive, punky boutiques adored by pop stars like Gwen Stefani and Courtney Love. The scene on this Sunday does not disappoint: It's like 250 music videos happening simultaneously on a single street, and we spot teens in outfits that would humble Marilyn Manson and the entire cast of Hairspray. Incongruously, the early 1920s Shinto Meiji Jingu shrine and the peaceful garden that surrounds it are just steps from Takeshita-Dori—for those craving a reality check, or perhaps a schizophrenic attack.

I'm convinced that the hip but much more grown-up neighborhood of Ebisu can't possibly be as much fun as Harajuku, but I like the sound of Buri, one of the city's new tachinomiyas ("standing bars"). Tachinomiyas used to be frequented by working-class men after their shifts ended but are now being reimagined as Tokyo's answer to the intimate, epicurean tapas bar. Buri's back wall is lined with colorfully decorated "one-cup" sakes—single-serving containers that are in vogue here right now. We opt for a dry junmai sake from Osaka that's kept in a freezer at around 7 degrees Fahrenheit. Our server shakes our cups before opening them, giving the sake a frothy, milky density. Standing around our small table and watching the Japanese hipsters and expats trickle in, we snack on bright-purple pickled turnips and sweet sea-urchin sashimi.

One of Jean-Georges Vongerichten's favorite late-night soba-noodle joints, Matsugen Ebisu, is just a few blocks away. The chef is such a fan of this place that he's been in talks with its owners, the Matsushita brothers, to open a soba restaurant in Manhattan (plans are on hold at the moment).

Strolling over from Buri, we walk into Matsugen's dark, sexy one-room space and sit at one of four communal tables in front of a station where, during the day, chefs hand-roll the noodles in front of lunchtime guests. Though the vibe here is chatty and social, this is a place that inspires an almost meditative focus on the noodles. We try two styles side-by-side: inaka noodles, made from whole, hand-milled buckwheat seeds that are roughly ground to bring out more of the natural flavor; and rin soba, made with only the inside of the seed, which creates a thinner, whiter noodle. The noodles are nutty, delicate-tasting and pleasingly rough-cut, and they're served cold—the best way to preserve the soba flavor. Seasoned soy sauce comes on the side for dipping, and I alternate between running the noodles through the soy sauce and eating them plain—to savor and memorize the taste of a perfect soba noodle.

Day 3: Decadent Tofu, Pork-Innard Stew, Kaiseki-like “Kappo”

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