What does it includes

Hi,
I will be traveling to Japan next year for a little more than 2 weeks and have decided to buy the JR pass. I wanted to understand what does it includ, regarding the transportation alternatives available.

I guess it's important to say that I plan to stay in Tokyo and end in Kyoto but will travel around a bit with some side trips while in those two cities, but also to travel to Nikko and Takayama in between. So, do I need to buy something else besides the JR pass traveling in Japan, like traveling on the urban areas or so?

I've read that you need also a prepaid card like Suica to travel on urban areas, but I am not sure how it works really.

thanks.