JR has a rail (or something) system that runs in Tokyo. When I've visited Japan, I've always gotten a rail pass. When we're in Tokyo, we use the JR trains to get around the city. I think I've used another system once in four or five trips.

I don't know about the financial side (how much it costs to travel in Tokyo without the pass). Hopefully someone else who knows the local costs for getting around might be helpful on that.