mari's passport is (almost) in hand
It turns out that we've been waiting for a passport that's been with the local post office for a week!
We sent our passport back to the visa office in Tokyo on September 26. The visa office, to their credit, essentially turned around the passport with the visa inside within a day of receiving it, and mailed it off on October 5. They sent it as a trackable mail item, but not requiring signature or by courier etc. It appears to have turned up on October 12, and then, in one of life's little magical moments, the attempt-of-delivery notification simply never got into our hands.
It was only because I'd asked our MP to look into it that I learned all of this. I went last Thursday (the day after the failed delivery, naturally) to ask them about speeding up the process of getting Mari's passport back. The visa office (which doesn't respond to applicant emails) told the MP's office the tracking number and I've managed to find out that the thing still at our local post office. They apparently never tried to contact us about the failed delivery even when they'd been hanging onto it for more than a week.
It's been over six months since we filed the application for Mari's permanent residency. I cannot believe what a mickey-mouse operation this whole immigration process is.

