Tokyo subway

Just to clarify what you're referring to, Tokyo Metro (hereby TM) is separate from JR, but both operate stations in the city, usually in the same general building. It's very likely you'll need to at least get a cheap ticket (~160 yen) from a TM station to the nearest JR hub from time to time.

JR passes cannot be used to access TM trains.

Hi there,

Yes, @sdash is correct. You can also get a pre-paid electronic travel card called a Suica or PASMO that can make travel on the metro easier as you don't have to worry so much about buying tickets. We have a blog post on using these cards online.

Hope this helps!