Hi, Japan is full of nature and cultural attraction, you may consider to visit following places :
Kyoto : the original capital of Japan, full of cultural diversity and shrines.
Nara : Neghibour city of Kyoto, world heritage shrine is there.
Hiroshima : visit for atomic bomb memorial and beautiful "dori in sea".
Mount Fuji and 5 lakes area : Must visit area of Japan to observe nature at its best.
Okinawa island : awesome beaches on crystal clear sea with beautiful coral and sea animals.
Osaka : see this https://www.tripoto.com/trip/the-tale-of-three-cities-osaka-kyoto-nara-part-1-5ac846a73f6f3