Conrad Harlow is released from prison because he was convicted of a murder that never happened since Emily Byrne is still alive, but he will be tried for her abduction.
A woman named Kelly Price shows up at Boston PD and tells Det. Gibbs that Emily was never kidnapped. She claims to have seen Emily two weeks ago arguing with a man at the marina. She identifies the man as Robert Semarov.
There are no fingerprints on the card and flowers sent to Emily, but the water in the vase is the same water that was in the giant tank where she was found. Detective Gibbs and members of the FBI begin to think that Emily abducted herself and killed Semarov. Nick gets her an attorney when they call her in to be questioned. Emily is horrified, but they don’t have enough to arrest her. Nick asks to help, but she tells him to work the case.
Emily tells her psychiatrist that she’s angry with Nick because he chose someone else. The doctor points out that Nick never made a choice. He thought Emily was dead.
Emily visits with Flynn who is beginning to soften but later she hears Alice voicing concern to someone over the phone that she doesn’t think Emily seeing Flynn is best for Flynn. Later Alice tells Nick that Emily makes both she and Flynn uncomfortable. Alice also thinks someone has been lurking outside their home, but Nick dismisses her concerns.
Nick and his partner follow Kelly Price. They get her fingerprints and find out she’s really Regina Talbot who has been arrested for drugs and money laundering for the Russian mob. One of her known associates is a Jonathan Cooper who works at a florist. When they go to question Cooper, he makes a run for it and then opens fire. When they finally capture him, he tells Nick that Regina worked for Semarov and was helped by a crooked Fed in the Boston office.
Emily break into Conrad Harlow’s plays and confronts him as he swims in his pool. She wants to know how he did it and who helped him. He tells her the answers are in her head, if she could only remember. Then the Boston PD come and arrest Emily, but when Conrad doesn’t press charges they let her go. While in custody, Emily asks Det. Gibbs if he’s a cop who closes cases or solves them. The two appear to bond. When Nick comes to pick up Emily, he tells Gibbs to ask Kelly Price about Regina Talbot. Gibbs calls Kelly Price and finds her phone has been disconnected and she’s disappeared.
Nick tells Emily about Regina Talbot and how someone at the FBI helped her change her identity. Emily says that when she was investigating Semarov he was always one step ahead of her and she began to suspect that he had inside information. Nick thinks they should figure out who the crooked agent is in the FBI first. Then he drops Emily off at her brother’s house and heads home.
Later that night, Conrad Harlow is found dead in his pool.