The book ends with June and Day together, running from the law and planning to go to the waterfront to pick up Eden before crossing the border and going into Colonies territory, which signifies a fresh start for all the characters. The end of the book is rather symbolic because it demonstrates that even though June and Day started off in completely different places at the beginning of the book—one of them revered and the other hunted by the Republic—they wind up in the exact same place with the exact same plan at the end:
We lie there together, watching the lightning and listening to the thunder, and waiting for the beginning of a rainy dawn. (2.18.32)
Despite how different their lives seemed in the beginning, June and Day now share their plights—so the dawn is a rainy one because even though a new day has arrived, it doesn't come without its complications. Eden is still in custody, the Colonies are still across the border, and June and Day are both mourning the loss of beloved family members. But they're ready to face the next challenge together.
The ending is also a cliffhanger. We're waiting to see what happens to the main characters as they cross over into the Colonies—and into their next adventure.