Quantum Tangle by Chris Reher

Dropping out of sub-space into the wrong galactic sector, Sethran Kada wakes up with a headache and an extraordinary alien aboard his ship.
She implores him to help stop the abductions of her people, an enigmatic species emerging from sub-space. When contact with her kind turns pilots into casualties, the Governors fear an imminent invasion engineered by their rebel enemies.

Pursued by Air Command, Seth heads deep into rebel-controlled territory to recover the stolen entities and keep this potential weapon from falling into the wrong hands. Things get personal when his alien visitor begins to transform his mind and his life, turning the rescue mission into a fight for survival for all of them.