Ferries can be a way of getting somewhere, if you do not have time to do a loop ride. For example, there are ferries that sail between Tokyo and Hokkaido, and any other number of other places. You could take a ferry from Tokyo, and ride back. Or, if you run out of time, chances are you can find a ferry to get you back days earlier than you could ride. Or just cut out a portion of the return leg if you want.
Ferries can be a time to relax and rest.
The way it works is you get your ticket and with it a slip for the bicycle. Then you go to the head of the line of cars and trucks that are waiting to board the boat. After the ferry is unloaded, someone will check your slip to verify that you paid passage, and a seaman at the entrance will wave the motorcycles and bicycles on. You ride up the ramp, onto the ship, and another seaman will point you to the spot where you are to lash your bike to a wall. There is always something to lash the bike to, and often the seamen will want to put his rope on the bike to, even if you secure it with your own.