Below is a map of Tokyo’s railway system. Needless to say, it is quite complicated BUT it will get you almost anywhere on time. If you are in Tokyo, I 100% recommend that you utilize the train / subway system to get anywhere.
Image taken from: http://www.meik.jp/2rosenzu/01_tokyo_rosen.html
Best option to get around Tokyo! Even if something looks far, if you take the train you can cover a lot of ground in a day. Trust me, the trains in Tokyo are fast.
Be mindful that the last train for most lines are usually around 12:30am!
There are A LOT of railway companies in Tokyo, all of which own multiple train lines, and have their own entrances/exits. Even if your transfer is at the same station, you will have to exit the station and re-enter the station for your next train from another entrance if the two trains are operated by different companies so be careful when entering!
Just some of the many railway companies in Japan (source: https://www.ohakojp.com/post/japan-s-train-system-a-beginners-guide)
Although this was not always the case, Google Maps has recently gotten really good at giving train navigation in Japan. The best way to check if your two connecting trains are operated by the same company is to check the icon:
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