I find myself taking the trains less and less these days. There's just too much cool stuff to see walking from spot to spot. The trains are great, but when you take them you're like a mole popping up at different points, and you don't see how neighborhoods connect. Some of my favorite areas are the "netherlands" - around 15-20 minutes from a station.
Anyway, plenty of cool areas are easily bridged on foot: Koenji to Nakano, Shibuya to Harajuku, etc. Today, I was a bit more ambitious. I wanted to walk from Third Uncle (near Koiwa station) to Shinto Gangu (near Aoto). These are kind of a pain to connect via train, since they aren't on the same line or even the same railway. But thanks to Google Maps, plotting a walking route wasn't too hard. I printed three maps but wound up chucking the first two, since the topography was easy enough.
Basically, you go west from Third Uncle until you hit a river. Then turn north. Just after you see a large fork in the river, cross the bridge and go straight. You'll see Shinto Gangu 5 minutes later. Easy enough, but just in case, you might want to print a couple of Google Maps (both places are plotted on my Tokyo toy shop map). Also, a compass always comes in handy.
Total walking time: 45 minutes.
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