I booked return flights online and then booked hotels and train travel. It's a great place to visit. Prices are commensurate or cheaper than the UK. In Tokyo, we stayed in Akasaka and then travelled to Kyoto, Osaka and Nara, flying into and out from Tokyo Narita. It depends on what you're interested in. You can only buy the Japan railcard before you travel but it's a great way to see the country and the trains are beyond lovely to travel on. Travel within cities is incredibly cheap by tram and train.