The pass covers JR lines and some ferries throughout Japan. Consequently, the pass covers JR lines in Tokyo too. The bigger cities like Tokyo, Nagoya, Osaka and Fukuoka have lots of private (non-JR) lines and subway systems - none of which are covered by the JR Pass. For getting around in Tokyo, you’ll more than likely end up taking the subway/metro. The only JR lines serving central Tokyo are the Yamanote Line, the Chuo Line and the Tokyo Monorail. Nothing to worry about though - just get a Pasmo/Suica and charge it up. You’d be hard pressed to spend more than 1,000yen/day on travel within the city. If you’re staying in Japan for longer than the 14 days of your rail pass, you should consider carefully when you activate your pass. Your rail pass works out to 3,375yen per day, so it’s better value to use a Pasmo/Suica if you’re only planning seeing the sights within Tokyo.