If you need a visa even as a short-term visitor in Japan, the period of stay can be 15, 30 or 90 days. If the period of stay is 90 days, you can legally stay in Japan for 90 days.
Even so, if you wish to stay in Japan as a short-term visitor till the end of the period of stay from the second time and on, please be careful.
Here is an example:
If a foreign citizen wants to come to Japan to see his or her Japanese spouse without a Spouse Visa, in other words, as a short-term visitor because he or she is in the middle of applying for a Spouse Visa, he or she should be careful from the second time and on.
If he or she applies for another Short-term Stay Visa, the consul might ask you why he or she stayed in Japan till the end of the period of stay last time. Even if he or she is in the middle of applying for a Spouse Visa and really wants to see the Japanese spouse, another Short-term Stay Visa might not necessarily be issued.
Second, even if a Short-term Stay Visa is issued for the second time, the immigration officer at the border has the power to decide whether to admit him or her. The admission is not necessarily guaranteed even if he or she explains the circumstances.
If he or she wants to come to Japan again as a short-time visitor after the first visit, I can explain the circumstances by issuing a document with my stamp on it to facilitate the process. Even if that document is issued, another Short-term Stay Visa might not necessarily be issued, and the admission is not necessarily guaranteed, but that percentage might get much higher.