The JR Pass is a special pass available only to those entering Japan on a tourist visa. It allows for unlimited travel around Japan on JR lines usually at a price much less than purchasing individual tickets.
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I'm half-Japanese so go there frequently, but every time it's a wonder and a joy. Japanese food is amazing - make sure to try traditional kaiseki where the chef serves directly to you, and don't be afraid to duck into non-chain restaurants as that's where you'll find the best places. If in Kyoto, try Ponto-cho, and if in Tokyo, make sure to visit Kabukicho and try the tiny bars.
If you're planning to travel around the country, definitely buy a Japan Rail Pass as it'll save you loads. If you're staying in Tokyo, there's probably less incentive, as there are a limited number of lines you can travel on with the JR pass. But it's great value, and the people at the Japan Travel Centre in London are so lovely and helpful.