Kyoto asks for early mornings. We walked the temple paths before breakfast, when the light is soft and the gravel gardens are still being raked. By mid-morning the famous sites fill, so we used the afternoons for smaller neighborhood temples and long, unhurried meals.

Nagasaki surprised us — a port city of hills and harbors with a layered, international history. The Peace Park is a profound and necessary visit. We left more thoughtful than we arrived, which is, I think, the point of going.

We brought our son to Hiroshima deliberately. The Peace Memorial Museum is difficult and important, and we are glad we did not shield him from it. Afterward we took the ferry to Miyajima and let the sea air and the deer return some lightness to the day.

We saved Tokyo for last, and it was the perfect crescendo. We oriented ourselves by train lines and neighborhoods rather than a checklist — an afternoon in old Yanaka, an evening among the lights of Shinjuku. The city is enormous and somehow never overwhelming.

Eat at counters. Some of our happiest meals were eaten elbow-to-elbow at tiny eight-seat restaurants where the chef cooks an arm's length away. Department store food halls are a wonderful, low-stakes way to graze.

• The rail pass pays for itself quickly if you are moving between cities — activate it on arrival.
• A prepaid transit card (Suica or ICOCA) makes local trains effortless.
• Carry a small bag for trash; public bins are rare and you will accumulate it.
• Cash still matters at smaller restaurants and shrines.