The National Museum of Nature and Science is split between the Global Gallery and the Japan Gallery, but it’s the Japanese building that’s a delightfully only-in-Japan view of the natural world.
The Global Gallery focuses mostly on biodiversity and evolution, and the exhibits are quite ingenious.
Open: Every day, except closed Mondays (but if Monday is holiday, the museum is open on the Monday and closed on Tuesday), and also closed from 12/31-1/3
Hours: 9:00 – 17:00, open late on Fridays until 20:00
Admission: Adults: ¥620, Children (up through high school): Free
Read a novel set in Tokyo