What should I do or go while I am in Japan?

I am going on a two week business trip with the company that I for to Kyoto, Japan in September. I will have three days to go sightseeing and do whatever I want, and I was wondering if any of you had any ideas where I should go visit, and what I should do. I am planning on visiting some shrines, and an onsen (hot spring). So what are some things I should add on my list to do?
Also I am asking this in the social section because I would love to hear some of you stories, if you’ve ever been