Abducted. The Great Deception Series, #1

Guilt and ghosts plague Calista Evans, the result of a desperate act she committed as a teenager. Eluding the law, she accepts a position in an underground bunker, growing food for the elite hiding far beneath the earth's surface to avoid a coming global catastrophe. Calista meets handsome John Becker at her new position, who claims to love her. But he doesn't know her past. Then, a coworker loses all traces of humanity overnight.
He's now more robot than human thanks to a brain chip implant. To their horror, Calista and John realize the elite, with the help of mysterious aliens, plan to chip all workers the same way. By chance, Calista discovers a possible escape from the bunker. But can she and John get free in time before they lose their humanity and free will forever?