A typical Japanese breakfast consists of rice, miso soup, grilled fish, pickles, a sour salty umeboshi plum and fermented natto soybeans. Natto is infamous for its pungent odor. Mix the natto with soy sauce and a bit of spicy mustard. It is sticky and difficult to eat, but goes well with rice. Go native and mix the natto with a raw egg and slurp it down!
Some ryokan may offer the option of a Western breakfast, usually including a scrambled egg rather than a raw one, and toast instead of rice. Coffee should be available upon request. However, ryokan may not be able to accommodate diet restrictions.
Nowadays, a lot of inns have switched from serving breakfast to offering a breakfast buffet. In such inns, feel free to help yourself to as much as you can eat without leaving any food on your plate. With each trip to the buffet take a clean plate.