The trucker agrees to drop Emily off in Boston. In Boston she breaks into Jack’s apartment while he’s not there. She hides a cell phone in his corn flakes, then she tries to use his computer to track the serial number on the pacemaker from the body.
While on Jack’s computer, an online chat activates. Someone is asking if Jack had a good time last night. He replies, not really, “bound and drowned” and offers to send the person the video. Then Jack types back, “Roses are red, violet is blue.” And the person asks if she’s still his favorite flower. Then Emily finds hidden videos on Jack’s computer of women being sexually tortured, some using water. When a neighbor hears the screams from the video, she calls the police and Emily runs.
The medical examiner says that the skeleton found in the woods had its orbital bones cut by a knife. This could have been the first victim. Agent Crown thinks that Emily has been Conrad Harlow’s accomplice for years, long before her abduction, and that's why he originally asked to work the case.
Nick learns that Emily was the only person to question the first witness to give them Conrad Harlow’s name as a suspect, and days later, that witness died of an overdose.
Nick comes home to find Alice leaving with Flynn. She says she’s headed to her sisters and was going to leave him a letter. She also tells him that she’s pregnant but she doesn’t want to be his second choice. She tells him to close the case and then they’ll talk.
Gibbs and the Boston PD search Jack’s empty apartment for signs of Emily and find Jack’s videos. Gibbs calls in for a warrant. They find the videos, the chat that Emily saw, and proof that Jack opened bank accounts with large amount in them just before Emily was abducted, but they can’t figure out how they were funded.
Gibbs talks to Jack’s former employer. He was fired for showing up drunk for a surgery and for multiple unexplained absences. After Emily disappeared, Jack wouldn’t show up for work sometime a week or more at a time. The employer also says that someone was embezzling funds. The hospital was paying for medical devices that they never received but they could never prove who it was. Jack is now working for a medical device wholesaler.
Emily follows Jack to the woman he was texting and watches as they have rough sex through a window. Emily follows the woman, Violet, to a strip club. She corners her in the back and questions her. Turns out that she and Jack saw one another for almost two years, but then he stopped when Emily went missing. He didn’t call her again until the day Emily returned.
One of the bouncers finds Emily and pulls his gun. It starts a fire fight in the strip club. Emily runs but is shot as she leaves. Emily’s face shows up on the strip club's video feed and the police head to the scene. Violet calls Jack and tells him about her talk with Emily.
Cadaver dogs uncover multiple decomposing bodies buried in shallow graves at Nottingham Park.
Emily calls Jack and gets his voicemail. She’s bleeding badly. She tells him she’s with Mom, and she needs to know why he did what he did. She asks him to come to her.