The Japan Rail (JR) Pass covers the journey toward Mt. Fuji, but it does not cover the final "local" legs of the trip. To reach the popular Kawaguchiko area, you can use the JR Pass for the JR Chuo Line from Shinjuku to Otsuki. However, from Otsuki to Kawaguchiko, you must take the Fujikyu Railway, which is a private line and not covered by the JR Pass (though the "Fuji Excursion" train runs the whole way, JR Pass holders must still pay the "private track" portion of the fare). For the Hakone area, the JR Pass covers the Shinkansen to Odawara, but the subsequent "Hakone Tozan" trains and cable cars are not covered. Furthermore, local buses that take you up to the 5th Station (the climbing start points) are never included in the JR Pass. While the pass gets you most of the way from Tokyo or Osaka for "free," you should budget for these extra local transport costs to reach the mountain itself.