Shinjuku, Tokyo, things to do: A walking tour reveals the secrets of city's busiest district

Megumi has a warning for me as we round a corner, as we turn from a wide, well-lit street into a smaller alley, as the crowds around us are funnelled together and the touts in their neatly pressed suits are forced closer to their prey. "From here," she says "it gets a bit … shady?"

Yes, shady is the right word, I assure her. That's the one she'd been looking for. It's also the one Shinjuku, the bustling transport hub and infamous red-light district in western Tokyo, is known for. This is a notoriously shady part of a generally non-shady city, where gentlemen's club touts entreat you to enter, where karaoke parlours look like fronts for something else, where photos of escorts, male and female, beam down from backlit signs.

Shinjuku is also peak Tokyo; it's everything you imagined. It's a galaxy of neon lights. It's big screens that shout advertisements from skyscraper walls. It's a labyrinthine train station that envelops you in underground arms and never lets you go.

It's intimidating. It's bold and brash. It's also, I'm about to find out, a place with a warm heart, where you can cloister yourself away from the brassiness of the greater suburb and indulge in everything Japanese nightlife should be about.

For that, however, you need expert guidance, which is why I have Megumi – or just Meg, to her friends. Meg is Brazilian, born to Japanese parents, and has been living in Japan for 12 years. She's moved around the city a bit, she says, but now resides here in Shinjuku which, her friends think, makes her pretty "shady" as well.

But Megumi wouldn't live anywhere else. Shinjuku is endlessly interesting; it's a city within a city, a place that can blind you with its bright lights, but charm you with its secrets.

And Shinjuku does have secrets. The first stop on our tour is an izakaya – Japan's answer to the tapas bar – in Sanchome, a quieter side of Shinjuku. "Please don't mention the name of this place," Meg asks as we step inside. She's happy to share it with friends, she says, and clients, but not with the wider tourist stampede. I can see why. Inside it's warm and friendly, with groups of friends and colleagues huddled around small tables, drinking beer and sake, eating small plates of good food. Meg and I grab a few snacks: burdock root simmered in dashi; goya, a bitter melon from Okinawa, served in a salad; large slices of raw buri, a type of fish, to be dipped in soy.

This is not the Shinjuku I know. It's quiet. It's refined. It's also soon time, however, for us to move on, to wander through Sanchome and out into Shinjuku proper, past the train station, through Omoide Yokocho, otherwise known as "Piss Alley", an impossibly narrow lane filled with yakitori restaurants, before we emerge near Kabukicho, the true red-light district.