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Visas and Immigration
A sasho (visa) is one of those necessary evils required for going international. Hopefully, in the future it will be possible to simply live as a world citizen and only need a visa for interplanetary travel. In the meantime, if you are headed to Japan and want to stay longer than 90 days, you will need some type of a visa obtained through a Japanese consulate in the United States. Your actual zairyu kikan (period of stay) in Japan and your zairyu shikaku (status of residence) will be recorded in your passport by an immigration officer at the airport where you land. A landing permit will be stamped in your passport, and your date of entry and the duration of valid stay in Japan will be written in as well. Make sure not to overstay your welcome!
One more critical point: Check that your passport is valid for at least three months if you're arriving in Japan as a temporary visitor (90 days or less), and at least as long as the visa status and length of stay for which you're applying. You could be denied entry when you land if your passport expires sooner than your allowable period of stay.
(excerpt from p.81)