Welcome to the site.
Tokyo huh? Well, I'm thinking there shouldn't be a shortage of healthy food available to you.
A good place to start is getting your diet in order. I personally like
www.FitDay.com for tracking food (it's free). It will help you get an accurate idea of just what you are eating, where your strengths and weaknesses are. From there, you can have a better idea of what to change. It's a bit tedious at first, but well worth the time it takes to enter everything, and it's a snap once you're used to it.
As far as exercise, if you want to be a runner, start walking/running, as long as there are no medical conditions coming into play. Start out small, and work your way up. I highly recommend beginning strength training as well, it will help you tone up and start to lose fat (the more lean muscle mass your body has, the more calories it burns).
You can do it, you just have to commit.