Take the monorail to connect to the main train line loop around Tokyo.
From there, go to Shinjuku. Then, Harajuku. While you're in that area, also check out the Meiji Shrine.
Depending how much time you want to spend, she might enjoy the kitchen/restaurant shopping district called Kappabashi.
And just because it's such a unique thing, she might enjoy the Akihabara Electronics City.
Akihabara and Kappabashi are closer to each other, Harajuku and Shinjuku are close to each other. But those two groups are on opposite sides of Tokyo from each other. So it kind of depends how much time you want to spend riding trains around.
I worked with a sales rep a few years ago who lived in a town outside Tokyo that had their train station dedicated to Doremon. I'd have to look that one up though.
Looks like it's Noborito in Kawasaki. But this article is from 2019 so don't know if it's still there.
https://www.moshimoshi-nippon.jp/198439I went on a sales call in Kawasaki in February 2020. I can say that once you get that far out, it gets very Japanese very quickly.