Tokyo has one of the most confusing mass transit systems I’ve ever encountered. It’s not surprising considering you have at least 3 distinct subway providers (note I said providers, not lines) and local rails. This means there are at least a combined 20 subway/train lines covering the city.
You have to understand thought, with 13 millions people living in Tokyo alone, talking the car is not an option. An approximate daily ridership of 8.6 millions (more than twice the population of Montreal), the system must be efficient.
Lets start with the subway map.
You’ll notice that the lines are divided into two providers, Tokyo Metro and Toei lines. These are the two main providers for subway in the Tokyo area. Price schemes are variable, depending on which station you are starting and where you are going. There is a special transfer service for people transferring between the two providers. Note that having multiple lines at a station does not indicate an easy transfer. I’ve seen subway lines connected by a 850m walk (10-15 minutes). My favorite transfer is at Awajicho, where you need to exit the station and walk 300m outside to catch your transfer. Then there is the Keiō line, which is operated by a third party and serves the western part of town. You’ll need those trains to reach the Square-Enix store.
Next is the JR lines.
The JR lines will get you pretty much to the same places, but often with more of a walk. I found myself sticking more to the subway during my stay, but I’ve been told using either is a matter of preference. The price schemes are variable again, and there are no easy transfers with the subway lines. Note that many JR line stations will not have English indications, so you might need help figuring out what your fair is. Popular stations in both systems are Shinjuku, Harajuku, Shibuya, Ikebukuro, Akihabara, Ueno, and Tokyo stations.
Finaly, if you need to get somewhere fast, you take the Shinkasen, the high-speed train in Japan. Although it’s pricy, it will get you there fast.
The Tokyo mass transit system might be complicated, but it’s efficient and easy to use once you get the hang of it. Just give yourself some time and you’ll be fine.