Spirits of Glory by Emily Davenport

One morning the people of the North woke up and the people of the South were gone. That s the first thing every child learns on the colony world of Jigsaw. But for one girl, knowing about The Disappearance is not enough. Hawkeye wants to know why.

That's why she spent half her life researching The Disappearance. And that's also why eight Neighbors show up on her doorstep, demanding that she accompany them into the Forbidden Cities ruled by the Southern gods to speak with the Spirits of Glory. Everyone thinks Hawkeye is an expert on Neighbors, these almost-humans who move, talk, and think as if they were born inside one of the Time Fractures. But she can't imagine what they want to ask the ghosts of their ancestors, or why they need her to go along. The Southern gods caused every human inhabitant of the Southern cities to disappear overnight :&emdash; what else might they do?

But the Northern gods say Hawkeye should go and her curiosity won't let her refuse, even though she's going into more danger than she can imagine. Pain and puzzlement wait along the broken interstate, along with scavengers who want to kill them all. Hawkeye's questions only generate more questions as they move farther and farther into the South, right into the heart of the Disappearance, until Hawkeye's questions have all been answered.

Even the ones she was afraid to ask

A unique, science fiction story about a young girl who goes on an incredible, fantastical journey at the request of the Neighbors to find the answers from the Spirits of Glory. The answers to why all the human inhabitants from the Southern cities had vanished. Along with her animals that are each their own character in this story, bandwagon on their quest.
A lot of details and specifics as you read, so it's important to pay attention. This is not a story that I could fly through and be able to keep all the details straight. I had to take my time.
Hawkeye is approached by the Neighbors because of her knowledge, intelligence and gifts. Hawkeye is young and smart, but not described as beautiful. She is one of the strongest and most admirable female lead characters I have read about. There is no romance in this story, but an introduction to a possible romance right at the end.
There is no way that anybody could figure out what was going to happen next in this one, no way you can guess the ending. There is magic, time fractures, intelligent animals, ghosts, Gods and the mystery that they have set out to solve.
I can tell you right now you have never and will never read a story like this one out there. I dare you to try to find one. Then come back and tell me about it!