The movie opens in an emergency shelter for what we soon learn was an earthquake. Reading up on the movie after the fact, Wikipedia points out that the movie was released a decade after the Tōhoku earthquake and tsunami (the most powerful earthquake ever recorded in Japan) in commemoration.
An old lady (Kiwa) at the emergency centre claims to be the grandmother of teenage runaway Yui and mute 7-8 year old Hiyori, and takes them home. Yui is suspicious of the old woman, but things go fairly well. But there's a lot more going on, and fantasy elements slide into the structure of the movie.
The movie is about finding hope after catastrophe - and it's heavy-handed abut it. The artwork is often very pretty, but the juxtaposition of young children, a magical house, a granny of unusual powers, and multiple Japanese spirits was a little too reminiscent of Miyazaki's "Spirited Away," and this movie doesn't fare well in the comparison. If I hadn't known "Spirited Away," I probably would have rated this as "pretty good." But standing beside that work of art, this appears pretty, sweet, and mildly disappointing.