When Agent Emily Byrne is rescued after years of captivity, she struggles to readjust to normal life as she learns that everyone has moved on from her apparent death. As the FBI finds a connection between Emily's kidnapping and one of her cases, an unexpected twist raises suspicions around Emily.
Conrad Harlow's release sparks erratic behavior in Emily, which doesn't help the suspicions around her. A new witness implicates Emily even further with her testimony, but Nick grows to doubt the truthfulness of her statement.
As evidence piles up against Emily, Nick desperately tries to prove her innocence. Emily and Nick grow suspicious of Adam. Alice clashes with Nick over the effect Emily has on their family.
With an arrest warrant issued for Emily, she goes on the run in an attempt to get more information about Adam's involvement in her kidnapping. Nick finds himself in a tight spot, both personally and professionally, due to his association with Emily.
Emily seeks to uncover the truth about the bleeding eye she keeps seeing, but the search only brings up more questions. Alice and Nick's relationship faces a major hurdle as the former notices Nick's feelings for Emily.
As Emily's investigation unearths disturbing evidence that casts doubt on someone close to her, Nick traces Emily's old investigation of Harlow, which only seems to implicate her further.
Emily is forced to confront her past as her investigation reveals a connection to a face from her childhood, but the disturbing details she discovers offer no comfort or answers.
With Nick's faith in Emily shaken, he joins the search for her in the hope of retrieving Alice and Flynn. Emily tries to get information from Charles, but the visit leaves her in a standoff with Nick.
Alice and Flynn's lives hang in the balance. Jack helps Emily uncover some new information about Charles and Dr. Shen. Nick and Gibbs finds clues that suggest that Emily might be more dangerous than they thought.
The truth is finally revealed as Emily comes face-to-face with the real perpetrator of the murders, but the confrontation puts the life of someone Emily cares about on the line.