On day 3, you have some decisions to make. Spectacular natural scenery or spectacular man-made scenery?
For natural scenery, you should probably head to Hakone, the best place for views of Fuji. Here you can enjoy amazing views of Fuji across Lake Ashi. You can also take ferry rides or cable cars to get an even better view! (Please be aware, the JR Pass only takes you as far as Odawara station, from there you will need the Hakone Free Pass which costs around £30 and gives you unlimited access to the transport around Hakone, including the ferries and cable cars.)
For culture, shrines and temples, make your way up to Nikko, known as a centre of both Shinto and Buddhism, magnificent temples and shrines sit side-by-side in this amazing home of Japanese spirituality. The mausoleum here to one of Japan's most famous Shogun's is one of a kind, and truly astounding.