The Fractured Mate by Susan Trombley

As a captive of aliens, Paisley is forced to work as an engineering assistant on an ancient wrecker starship. She knows she has to keep her head down and her behavior humble in order to survive.
When the crew responds to an automated distress call from an Akrellian warship that shouldn’t be malfunctioning, she senses a threat, but she knows no one will listen to her warnings. Paisley realizes that her days of avoiding danger are over when, among the rescued passengers, trouble with a capital “T” is escorted onto her ship—in chains for bringing an apocalypse to Earth that resulted in millions of deaths.
Something about the prisoner makes it impossible for her to look away from him, and it isn’t just the fact that he’s the most handsome alien she’s ever seen. Yet, when he meets her eyes, there’s a darkness in his intense gaze that makes her think his captors might be telling the truth about him, despite his claims of innocence.
Caught between two greedy groups seeking wealth and power, Paisley soon discovers that far more lies behind the mystery surrounding the Iriduan prisoner they call Halian. He might be stealing her heart, but she can’t keep him in chains, because he could be the key to saving the galaxy—or destroying it.
This isn’t a light read, featuring a sweet-from-the-start hero. The main male character has villainous facets to him that do not immediately soften in this slower-burn romance. The journey to love will be very rough at times.