The media makes the assumption that Emily Byrne is involved with the six bodies found in Nottingham Park, but the FBI and Boston PD won’t comment. 

Emily wakes up in a motel room after Jack has performed surgery to remove the bullet and save her life. Jack says his unexplained absences were actually him in rehab after she disappeared. She asks him to help use the pacemaker to find the identity of the body in the park.

The body belonged to Dr. Lu Fan Shen who was an administrator at Barrett House, the orphanage where Emily lived. Emily tracks down Shen’s brother, Eric. Eric says Dr. Shen was kicked out of MIT because his behavioral work was deemed too controversial, but that working at the orphanage gave him joy. He keeps his brother’s research in storage. 

In the storage unit, there are lots of files and audio cassettes. While Emily listens to a cassette of a little girl being forced into a tank for an experiment, she is grabbed from behind. 

Emily wakes up in a van and hears two men arguing over turning her in for the $250,000 reward. When they get into an accident, Emily is able to jump out and steal the other person’s vehicle to get away. 

Gibbs realizes that Jack’s extra bank accounts were to pay for hookers from Sevarov’s club.  When Jack goes to an Alcoholic’s Anonymous meeting, the police arrest him. 

Emily goes back to the storage unit and gets her gun and the recording. The little girl begs for the experiment to stop, but he tells her the only way it will stop is if she helps do it to someone else. She hears Dr. Shen call to someone named Charles and Emily remembers a fight with Charles as a child. 

Flynn gets into a fight with some neighborhood kids when they tell him his mother is going to end up with a bullet in her head and he’s going to grow up just like her. Flynn believes that his mother is innocent and alive. Nick backs him up. Nick asks Alice to come home but she refuses. 

Nick goes to Alice’s sister’s home to visit with Flynn, but he finds the front door broken and the house a mess. No one is there, but there’s a cell phone on the floor with a video of Emily cued up. On it, Emily is telling Flynn that she’s still alive and that they will be together soon.