Wait for fireflies to glow over water at dusk
For a few weeks from late May into June, fireflies come out after sunset and drift as soft yellow-green lights over ponds and streams. Walk slowly along the water in a garden or at a shrine and wait for them to appear. The dates shift each year with the weather, so check before you plan, and keep flash and phone screens off so you do not disturb them.
During the shrine's firefly festival in June, which lasts about a week, fireflies glow around Yanagihara Pond, a quiet pond inside the grounds, and visitors walk a path beside it after sunset. It is a short walk from Kamakura Station, about an hour from Tokyo by train. The festival is cancelled in rain, and visitors are asked not to use flash.
Wild Genji fireflies, the larger of Japan's common kinds, drift over Horai-en, a pond garden next to the hotel, especially around its Horai Bridge. They are usually at their best from late May to mid-June and fly most from about 7:30 to 8:30 in the evening. Hakone is an easy day trip from Tokyo, but plan your ride back before you go, since you will be leaving after dark.
A large Japanese garden around a hotel in central Tokyo, where fireflies glow by the ponds and little streams on early summer evenings. It feels far from the city, with trees and water all around you. The firefly evenings are mostly offered with dinner at the hotel, so check its website each year for how to join.