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, maybe by someone in the FBI.
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.
When Detective Gibbs and Nick find an FBI agent who appears to have been murdered by Emily, the hunt for her goes up to a new level. With the help of a clue given to her by Adam Radford, Emily tries to tie all the threads while evading arrest. Nick tries to reconcile with Alice’s betrayal
Emily avoids arrest and finds another trace of 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? Alice gets bittersweet news and has to make a very difficult decision.
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.
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.
Emily is able to retrieve more information from Charles and hopes that this will be a breakthrough in her research.
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.