Trip cost - non covered station commuter pass

I am going to use a commuter pass but some times I might wish to exit from a non-covered station its only a slight deviation due to some time atrocious train line delays- how to calculate the cost if there is one?

You pay the cost of the section not covered by your pass.

IF there are massive delays (which I'm doubtful of in Japan in 99.9% of most times) unless there is some kinda of crazy natural disaster. I'm sure the rail companies wont be worried about the uncovered portion of your fare.

But also unsure and find it highly unlikely that if you are travelling using some form of a rail pass, that end up on another rail companies platform.

Keihin Tohoku was delayed indefinitely from its initial terminal in Omiya at least half an hour. I suspect suicide as cause but they didn't even have delay on their display boards as the timetable went to "hell"- I was changing lines as a station was easier to get home from so I missed that they missed their first departure time . It later said ready in 10 minutes and those 10 minutes passed and then 10 minute delay and then I gave up and took a different line. How do Japanese work it out- I could use a Japanese site- some must have say I always commute to Head Office but occasionally have to go a branch.

As Firas said, you basically just pay for the portion that is not covered by your pass. It should be automatically calculated if you use an IC commuter pass. Otherwise you'll have to stop by the manned gate to work it out.

Typically if there is a big delay on one line people may look to change to other lines, but it isn't always possible to go around a train delay. In that case you don't have too many options other than to wait it out, or maybe take an expensive taxi ride. Luckily these major delays are quite rare.

I case of natural disaster, then all the train lines will be shut down and your options become further limited until they are up and running again. With the 2011 earthquake that meant that taxis, rental cars and bicycles were almost immediately sold out, and many people ended up stuck in the Tokyo area overnight.

There is a natural disaster every 3 months that impacts Kanto- it closes a few railway lines but the system keeps going. Other non-natural disasters happen with some regularity and bad slowdown happen on multiple line. Their disruption management systems particularly JR are pretty bad. I want to calculate before I potentially do it.