OK - you don't seem to have much idea of what you want to do yet, so I'll just make one suggestion - take a look at this website:
Tokyo travel guide for essential sights & attractions in Tokyo Japan - UnmissableTOKYO.com
I've done most of the things it suggests and I can guarantee that they are all really great unique-to-Japan experiences.
Other than Tokyo, be sure to go to a hot spring resort at some time (Hakone is great, and very day-tripable from Tokyo). And Sumo will be on in January in Tokyo - be sure not to miss it.