For example, in my opinion the best way to explore Tokyo is to simply leave your hotel in the morning, wander around all day, and stop anywhere and everywhere that looks interesting. The excellent mass transit system means that it won't be a problem to get back.
In more rural parts of Japan, there are signposted walking trails. Here are three which I highly recommend, in whole or in part.
Yamanobe Road: https://www.japan.travel/en/destinations/kansai/nara/the-yam...
Kyoto Trail: https://kyoto-trail.net/trail_course_e.html
Shikoku Henro-Michi: https://www.henro.org/shikoku-pilgrimage/map
These places are wondrous for their natural and human-made beauty, and have tons of temples, shrines, and historic sights along the way. I strongly second Patrick's advice to get out of the big cities, and virtually anywhere you go you will find much that is beautiful.