Getting around Tōkyō, Japan is easy if you once understood the systems and know how to get a ticket. There are JR train, subway and bus networks – the latter you only need for more remote locations. Remember: you enter busses in the rear and pay when you exit in front.
The best option for me were the 13 subway lines provided by Toei and Tōkyō Metro. Buy a prepaid IC card (“Suica“) and swipe where necessary. The day passes typically don’t offer good value for money.