My son is in Sasebo now and just got a local phone. I have sent him a question about local options, will let you if he has any info.. We also use Facebook messenger for texting and video calls. My son did get a Google Voice number while he was still in the US. You need a cell phone to get it set up so it is easier to do while you are still here. He should then be able to make phone calls from his computer (or maybe even cell while he is on wifi) to US numbers. He set that number up to have in the event he needs to call his insurance company or other US based business. He has suspended his US cell phone line.

I realize you asked about International calling but in case he will be getting a phone in Japan to have a local Japan number, my son just told me: "Cost is about the same with the various carriers. The selection of phones is different. Big 3 are softbank, docomo, and AU. I've heard mixed things about docomo (nothing specific, just by reputation). Softbank is on base. Apparently Softbank has better coverage in Sasebo but can be spotty in the areas around it. I haven't had any issues with AU so far. Also AU was pretty easy to set up despite the language barrier as it is off base store."

Best wishes to your son - hope his travels are smooth.

I realize that this reply comes late and you may have already made a decision on what to do, but just in case you haven't - I spent a lot of time researching the best plan for my son to have while stationed in Yokosuka.  We eventually decided to do a military suspend on his Verizon plan and opened a Sprint plan while he is there.  They have something called the Japan plan for only $5/month more which gives him unlimited text and phone (incoming and outgoing) and supposedly a higher speed network.  Apparently everyone uses Facebook messenger to communicate on base.