If you plan to travel around Japan during the Rugby World Cup
you will need a Japan Rail Pass
With Tokyo or Yokohama as a base, you can organize daytrips from there and reach the other match locations by train.
To plan your journey and to check a train schedule, you can use Hyperdia
If you stay in Tokyo and Yokohama you may need a Pasmo Card or a Suica card. Learn more about the IC card in Japan