[Symbiote]

Many European cities compromise, by running trains overnight on Friday and Saturday nights, but using only buses on Sunday-Thursday nights.

(Tokyo seems not even to have buses running at night, which is really strange.)

[midoridensha]

No, the whole public transit system shuts down sometime after midnight. At that point, you can either walk, ride a bicycle (there are rental/bikeshare bikes available), or take a taxi.