Why not 'WWOOF'?
If you have a green thumb or are willing to do little labor in the rural areas of Japan in exchange for room and board, then it's time for you to sign up for World Wide Opportunities on Organic Farms (WWOOF). Being able to do organic farming in Ibaraki through WWOOF was an incomparable experience for me. As a "WWOOFer," I was tasked with assisting in the summer operations of a fish farm-cum-restaurant, where families paid to do some fishing, and then we prepared the fish for them and allowed them to enjoy the premises. While helping out in the kitchen—washing the dishes, cleaning the restaurant facilities and other minor work—I was allowed to eat anything I wanted and enjoy the carefree (and internet-free) farm life for a few days.
If you decide to do WWOOF, part of the arrangement is that you can take days off to explore the town, even as you stay on your host's premises.
Farm with Foreigners
If you are not exactly comfortable staying with a Japanese host family, fearing you may not know the language and culture well enough, there's Hackerfarm as an option. The group behind FarmLab, an experimental farm plot in Chiba, is composed of mixed nationalities. With a little negotiation, especially if you can contribute something or want to learn something about their methods of crop rotation, traditional cultural farming such as Japanese satoyama techniques, and companion planting, you may be allowed to stay on their farm grounds. Chiba is a train ride away from Tokyo, so this site is definitely a good home base for a few days.
Bond with Buddhist Devotees
If you want a truly unique experience as you visit or travel around Japan, you can book a stay in a Buddhist temple. On Mount Koya, in Wakayama Prefecture, you can bond with the monks of this tight-knit Buddhist community. The lodgings available in the area are all close to the quiet forests and sacred mountains. Although getting to Wakayama will take you two hours from Osaka, spending a few nights here is worth it, especially since it's considered a UNESCO World Heritage Site.
Go for the Great Outdoors
Japan has done a good job maintaining green areas in both cities and rural areas. To its credit, it has 17 well-preserved cultural sites and four natural sites recognized as UNESCO World Heritage Sites. When exploring Japan, there's an option to actually pitch a tent and enjoy the natural surroundings as you sleep and wake (in designated campgrounds though). There's Ama Camping Ground in Okinawa, for one. There's also Hikawa in Okutama, which is perhaps the nearest campground to Tokyo.
Book a Bed Among the Books
If you are quite conservative and not a fan of going too far out of your comfort zone, then perhaps you would like to stay tucked in bed with books. Just an easy train ride from the main Tokyo Station is Ikebukuro, a bustling Tokyo suburb with very dynamic shopping and nightlife. If you're an introvert, or your idea of rest after a long day of exploring is your version of a "bat cave" with books, then this bookshop accommodation in Ikebukuro is the perfect hideout for you. Book your stay with a bed nestled in books. Definitely one for the books!