Shadow Road by A. E. Pennymaker

Brenorra Warring's father is going crazy. That's the only conclusion Bren can come to when a fire destroys everything they own, and his only answer is to take a job in the uncivilized Coalition Colonial Region on the other side of the ocean. Then disaster strikes again, and Bren is left with nothing but the clothes on her back, the things in her father's satchel, and the discovery that he was lying about his reasons for leaving. When more of her father's secrets are revealed, it becomes clear that someone powerful is killing innocent people to keep those secrets hidden — and they are hunting for Bren. Now on the run, Bren is pulled into an alliance with two very different men. The first is fighting to bring down the same shadow organization stalking her, no matter the cost. The other is a brilliant but icy war hero who has been branded a wanted man by the enemy. With danger rising on every side, Bren must solve her father's trail of coded messages before the last of his secrets fall into the wrong hands. In the process, she will have to rewrite everything she once knew about her life, and reveal strengths she never thought she had.