Cycling is the most handy and free mode of mobility to get extraordinary experiences. It should be the best choice, if the situation allows you, to discover hidden elements of Japan which you usually miss in the other modes of travel. Cycling over country-side or urban jungles in Japan must bring you priceless rewards. Traveling around the entire Japan on a bike? Maybe the idea is too far fetched, but most of the local Japanese would be willing to help you accomplish such a crazy endeavor rather enthusiastically.
Japan by Bicycle
Cycle Around Japan:Noto Peninsula
Cycling "Length Of Japan" in October 2015
Japan: The Hidden Alps
Racing through the Holy Temple in Japan