Here are some simple drawings of map to illustrate how things are. 

In simplest way, Japan is like that...and so is Tokyo. And Motokyo is focusing on the east side of Tokyo in blue highlights, which is called 23 ku (ward or county for you). It's the most exciting area of Tokyo (no offense to the west side people).

Here is the east side of Tokyo. Basically, this is all you need to know (no offense to the west side of people) but this is usually the area people visit and people call it downtown Tokyo. Yamanote line goes around the Tokyo area, as long as you master how to use Yamanote Line, you should be able to get to most of places in Tokyo downtown.