People often cite admirably high-minded reasons for wanting to visit a specific foreign country. An interest in history or architecture, perhaps. A desire to walk in the footsteps of their favourite author or artist. Or maybe they want to make a musical pilgrimage to the spiritual birthplace of jazz.

Bully for them, but that's not me. I wanted to visit Japan because of a video game in which you had to jump over animated turds.

The game was called Kato-chan & Ken-chan – a cheerful platform game in the vein of Super Mario Land, except the lead characters urinated, farted and defecated throughout each level. Kato-chan & Ken-chan was one of many imported, inexplicable Japanese titles I encountered while working in a games shop in the early 90s. Mario and Sonic made sense to western players, but lurking just beyond these palatable mascots was a world of entertainment too strange to ever secure an official European release: fascinating, crazy games full of talking octopuses and jaunty tunes. American games were fun but bland. Japanese games oozed a demented spirit. Unfathomable, futuristic madness: that's what made me want to visit Japan.

A manga store in Tokyo. Photograph: David Levene/guardian.co.uk

Of course, it helps that Japan has, for years, been presented as a kind of Nerd Mecca. Not only is it the undisputed gadget capital of the world, it's a place where being a geek (or otaku) is comfortably mainstream. Former Prime Minister Taro Aso is an enthusiastic manga-collecting otaku, the TV ad breaks heave with glossy commercials for collectible card games, and multi-storey games arcades are commonplace. There's a gadget in every hand. Outside rush hour, the subway is eerily silent: thanks to a strong underground signal, everyone's staring at their smartphones, texting, playing games, or reading. Only after a fortnight did it strike me: not once did I hear a single person actually speaking into their phone on the Tokyo subway. Everyone – and I mean everyone – seemed to be perpetually tapping and swiping in silence. Unnerving to many: to a geek like me, it felt strangely comforting.

It's easy to find grand-scale geek spectacle in Tokyo: just hop on the monorail to Odaiba, a man-made island in the middle of Tokyo bay. There, nestled amongst a collection of Bizarro skyscrapers straight out of Starship Troopers, is Miraikan, the National Museum of Emerging Science and Innovation. Here you can watch celebrity robot Asimo go through his paces, or simply gawp in astonishment at the gigantic "geo-cosmos globe": an LCD-clad model of the Earth capable of depicting metrological data in real time. This is what Logan's Run would've looked like if they'd had more money and time. There are also a series of frankly baffling exhibits, including one which, apparently impossibly, projects a gigantic microbe-style creature around your feet as you enter. This virtual floor-dwelling entity then follows you around the room as you shuffle about, interacting with monitors with giant eyes on them, some of which offer to "turn you into a song". It's like a cheese dream on a mothership.

For a more down-to-earth nerd-out, Tokyo's Akihabara district is to geeks what San Francisco's Castro Street is to the LGBT community. It's an otaku paradise, an overwhelming whirl of shops selling electronics, games and comics. Any object you can conceive of having a USB attachment poking out of it is for sale, along with several hundred thousand that you can't.

I'd been looking forward to browsing the shelves for zany gadgets, but the reality was slightly disappointing. Smartphone apps have replaced many of the charmingly pointless Japanese gizmos that used to be pop up on late-90s travel shows. More significantly, the west has become overtly tech-obsessed too. At home, we're routinely battered over the head with so many miraculous widgets, a sort of amazement fatigue has set in. So while in Japan you can easily stumble across a remote-control tissue box or a battery-operated planetarium for your bathroom (by which I mean a waterproof Saturn-shaped orb that floats in the bath and projects the entire visible universe onto the ceiling), the sense of surrounding novelty has diminished. It's less "WTF", more "yeah, that figures". Touring the electronic shops is still an entertainment in itself: I was merely surprised to discover I didn't actually want to buy anything.

One of the few places I did want to spend money was in the arcades. In Britain, arcades have largely died out: we play at home, on Xboxes and PlayStations. Consoles are even more widespread in Japan, of course, but for many, finding the time and space to play in comfort is tricky. Home is often a cramped flat for all the family. Hence the evolving use of manga cafes (or mangakissa) for the nerd seeking a bit of peace and quiet. Originally these were internet cafes where otaku could gather to drink coffee and read comics: they've subsequently morphed into surrogate bedroom services. For an hourly fee you can hire a private cubicle containing a TV, a BluRay player, a computer, a games console, a stereo … everything you'd find in a techno-savvy twentysomething's home den, right down to the bed (increasing numbers of people sleep in these bedrooms-for-hire overnight: they're open 24 hours and are considerably cheaper than a capsule hotel).

Given this environment – herds of itinerant otaku wandering the streets – the continued survival of games arcades in Japan makes sense. But these are a far cry from the traditional British seaside arcade packed with flickery old Track and Field cabinets. These are bleeping, whirring, multistorey citadels filled with people doing things that scarcely make sense to an outsider. Let's run through a typical example, level-by-level …

On the ground floor: endless rows of what the Japanese call "UFO grabbers" – those familiar fairground games in which you make a doomed attempt to grab an underwhelming prize using a mechanised claw. They seem to love these things, despite the fact that to the best of my knowledge no human being has ever successfully extracted a prize from one. Failure booths, I call them.

Go up a floor and the crazy video-gaming begins. Given the competition from home consoles, arcade machines have to offer something different. Case in point: Cho Chabudai Gaeshi ("Flipping the Tea Table Game") which consists of an arcade cabinet with a small table attached to it. It's actually more of a stress reliever than a game: the aim is to vent your frustration by hammering furiously on the tabletop before tipping the whole thing over in a rage. Time it properly and you'll cause maximum on-screen chaos. My favourite level was set in an office, with the table doubling as a desk: upend your workstation at just the right moment and you'll send co-workers plummeting out of the window to their deaths.

Above that: a floor filled with super-advanced photo booths known as purikura – essentially digital dressing-up boxes. There are two main uses of a purikura: either jostle in with a bunch of friends to commemorate a night out, or, if you're a teenage girl and/or a psychopath, spend hours perfecting your costume before having your image digitally altered until you resemble a creepily infantilised manga cover girl.

Top floor: a roomful of sombre youths vying for individual supremacy using some form of networked arcade strategy game that uses collectible cards. Imagine witnessing a game of bridge being played in the Cabinet War Rooms in the year 2072 AD. Some of the games are based around recognisable sports (like football), others around ancient samurai conflicts – but whatever the theme, the nature of the action is absolutely impenetrable to the casual onlooker. The players may as well be communicating psychically. I had no idea what I was looking at: the one thing I did know was that this unfathomable futuristic madness was precisely the sort of thing I'd come to Japan to see. Somehow, I was home.

• Virgin Atlantic (0844 2092 770, virginatlantic.com) flies from London Heathrow to Tokyo from £846pp return. Mandarin Oriental Tokyo (00800 28 28 38 38, mandarinoriental.com/tokyo) offers rooms from £357 per night, B&B. Conrad Tokyo (+81 3 6388 8000conradhotels.com) has Bay View Rooms from ¥42,000 (around £350). The Peninsula Tokyo (+81 3 6270 2888, peninsula.com) costs from £374 B&B, excluding taxes, for a superior room.

Specialist operator Inside Japan (0117 370 9751, insidejapantours.com) offers small group tours, self-guided or fully tailor-made trips. Its 14-night Best of Japan self-guided holiday, which includes stays in the mountains of Hakone, on the island of Miyajima and in the craft town of Takayama as well as Tokyo, Osaka and Kyoto, costs £2,280pp, excluding flights and local transport. For more information go to the Japan National Tourism Organization website: seejapan.co.uk