After years of assuming FBI Agent Emily Byrne was a possible victim of serial killer Conrad Harlow, she is miraculously returned to her family. Emily, however, has to struggle with the mysteries of her captivity and the fact that everyone has moved on without her. When the FBI traces the sex trafficker, suspicion suddenly moves to Emily. Is she still the same person they knew?

Conrad Harlow is being released from jail, and Emily has not come close to solving the mystery of her kidnapping and time in captivity. As Emily struggles to return to normal life, a witness turns up and reinforces the suspicions of Emily. Emily denies the suspicions and is sure the witness is lying and was forced into making a false statement, maybe by someone in the FBI. Will Emily and Nick be able to find out the truth before Emily is again torn from her family?

Emily is now the main suspect for yet another murder and her time is running out. Can Nick and Emily find enough evidence to plead her innocence, or will Nick's clouded judgement be tested by the ever growing evidence being brought against her?

The evidence against Emily is too much for the FBI and Boston Police Department to ignore, so they ask her to turn herself in. In the midst of chaos, old feelings come to the surface between Nick and Emily. Emily decides she would rather flee and try to solve the mystery that is ruining her life. Can Emily save her relationship with Flynn? Is it possible for agent Adam Radford to solve this mystery? Can Nick trust Emily anymore?

Nick and Tommy witness the killing of an FBI Agent. They suspect that Emily did it and escalate the search for her. Emily uses the information from Adam's interrogation to unearth more evidence. Alice confronts Nick about Emily.

Emily avoids arrest and finds another trace of the investigation. But with the disturbing new evidence, Emily begins to suspect one of her loved ones. Unfortunately, he is the only person who can help Emily figure out the case. Could it be just a little paranoia from Emily, or does she not have anyone to turn to?