If you stray too far off the beaten path, you can find yourself in a rather unexpected sticky situation: JR East's “One Man Car” service. Some trains and parts of the JR East network are essentially disconnected from the rest of the system. What this means for you is that Suica doesn't work, but not only that, there will likely be no staff at some or all of the stations on your journey.
If the start station is staffless, you need a ticket of some kind. You have 3 ticket options if you're a foreigner, and 3 if you're a resident.
If the start station is staffed, you will need to purchase a ticket prior to boarding or obtain an entry record from a staff member. Almost all stations with staff members also have ticket vending machines.
With one of the above ticket options, exit the train near the driver door and present your entry option and fare, if necessary.
Though extremely rare now, some portions of the JR East network are entirely honor-system based. You need to deposit cash and your entry record in the exit station ticket box with your payment in this case.
If the end station is staffed, you will generally speaking present your fare ticket or payment option, or settle fare at the station with a staff member.
In the case where you're traveling between two unstaffed stations, you will be settling your fare on the train or showing permission to leave directly to the conductor. Please don't get into a situation where you board a staffless train with no cash.
Depending on the route you're on, you may find yourself in a situation where there are absolutely no announcements in anything other than Japanese. I recommend, in this case, that you pre-calculate where your stop is by the number of stops between you and your destination.
You can and will be taken to mysterious far off lands, aka stations of despair if you aren't aware of where you are going.