Thank you for the quick reply. That's a relief.
The last time I had an overnight in Narita (way back in 2005), I just got the visa on arrival at the airport. But from reading here it sounds like they are getting stricter, and for my passport (Indonesia) I'll need to apply for a transit visa in advance for the overnight layover.
If I miss the connecting flight to Chicago and have to stay overnight in Narita (with no transit visa since I'm not planning to stay overnight), will I have issue getting the visa on arrival? My son will not be an issue since he has a US passport.