Adam has an agent watching Emily, but they lost track of her and never her saw her break in to Adam’s home.
Nick takes Emily to see Flynn one last time before turning herself in to Boston PD, but Flynn is asleep. Nick tells her to go up and take a look at him anyway. Alice isn’t pleased as she thinks Emily is guilty.
They head back to Emily’s motel room where they break down and make love. Afterwards, when Nick uses the bathroom, Emily runs off. She later calls Nick and says she couldn’t handle being a prisoner again. She plans to solve this herself and begs Nick not to lose faith in her.
With Emily on the run, Adam suspends Nick from the FBI and takes his badge and gun. Nick accuses him of killing Conrad Harlow.
Emily finds Flynn at the pool and tells him she needs him to know that the things people are saying aren’t true. Flynn says he believes her. Alice finds them before Emily can get away. She says Emily doesn’t deserve Flynn and that she’s only hurting everyone. When Alice goes to call the police, Flynn stops her and Emily gets away.
Emily accosts Adam in his vehicle, causing the manhunt for her to widen. She calls Nick from her burner phone to tell him what she’s doing. He tries to talk her out of it but she hangs up on him. From the background audio, Nick figures out where she’s taking Adam and calls Gibbs to come with him as backup.
Emily remembers that Adam didn’t back her up when she followed a lead on Conrad Harlow and that’s when she was abducted. Emily continually puts his head into a pool of water until he tells her what he did to her. Adam says she kidnapped herself and that she was his partner. He admits he got Regina to lie to the cops. He admits that Semerov cut him in on the money laundering operation with Regina, but he swears he didn’t plant her DNA on Semerov. He really believed she killed him.
Adam says he was drawing bleeding eyes because he was obsessed with finding Emily after she disappeared. He believes the Bleeding Eye is a place, not an actual eye.
Emily realizes that there is a third person out there who is setting her up. Just as it looks as though Emily might let Adam go, they hear Nick and Gibbs arrive. Adam calls for help and Emily runs. Then, just as Nick and Adam show up, someone opens fire from the shadows, shooting and killing Adam. Nick and Gibbs both believe it was Emily.