Tokyo obviously, but the dotonburi (spelling?) market of Osaka is a must see. I’d also recommend Nintendo land at universal studios if you grew up in the 90s with those games, it’s incredible. And in terms of “plan before you buy the tickets” the Miyazaki museum is sold out months in advance, so many people will try to a reservation there before getting flights and hotels if they’re fans.

Aside from that, the deer in Nara are pretty special and it’s just a day trip from Osaka. And if you’re in the mood for something somber but incredible, Hiroshima is beautiful and the museum is incredible.