Emily’s alleged serial killer, 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.
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?
Jack helps save Emily's life and finds a startling connection with Emily's childhood. Emily discovers secrets from the past that relate to a childhood friend, Charles. Meanwhile, Tommy arrests Jack for helping Emily. Alice confronts Nick, which puts both her and Flynn in danger.
Alice and Flynn are abducted by a mysterious person. Nick suspects that Emily was the one who kidnapped his family and desperately tries to find them. A reporter assaults Jack every time she wants to get exclusive information. Emily tries to get answers from Charles, but has to flee when Nick tries to arrest her. How will the couple act when they meet again?
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?
Tommy makes a new discovery that puts a new light on the investigation. Emily's past faces the present when she finally meets her captor, and will be like the mouse and the cat. When Nick gets hurt, Emily has to face several situations to save the ones she wants.
Emily is able to retrieve more information from Charles and hopes that this will be a breakthrough in her research. Will this lead to Flynn? Will she discover the identity of who is after her? Will Tommy and Nick catch Emily and end the case that consumed the former agent's life?
Emily is now the main suspect for yet another murder, 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.
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
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.