The Master of Puppets (The War of Souls Book 1) by Molly J. Bragg

Jakari, an alien assassin, receives orders taking her to a primitive alien world. She expects the mission to be like any other.  Get in, eliminate the target and get out again.  Instead, when she arrives, she finds out that one of the leaders of the fascist Char Oram is there, seeking to turn the inhabitants into mindless soldiers that could tip the war in favor of the Char. Hayami Takahashi follows a strange woman down a dark street and all she wants is to make sure the woman didn't wind up as the next victim of a kidnapping ring working the streets of Dallas.  Instead, she finds herself in the middle of a civil war between two factions of shape shifting cyborg aliens. After Jakari saves Hayami from becoming a test subject in a Char lab, the two of them are working together to stop a war that's been raging for nine thousand years.