Emily sees a video of Nick saying he believes that she took Alice and Flynn and she’s devastated.
Alice and Flynn wake to find themselves locked up in some sort of basement where a mysterious figure leaves them water and moldy bread. When they eat it they end up drugged. A masked man takes Flynn out of the room, then he asks Flynn if he should hurt Flynn or Alice. Flynn choose himself and ends up in a tank similar to Emily’s with water rushing in and almost drowns. Later, Flynn is returned to Alice.
The reporter that Emily stabbed in the hospital, Laurie Colson, bails Jack out of jail. She wants and exclusive to tell Emily’s side of the story and leaves him her card. Jack talks to Emily and then goes to their father for help. Warren uses his old contacts to find that Charles Avallone from Barrett House is now being held at Edgewater Psychiatric Facility.
When Jack returns Warren to the assisted living facility, he’s warned that his father’s blood pressure is high and that he needs to avoid stress, but Nick shows up telling Warren he has to choose between protecting Emily and finding Flynn. Warren tells Nick that he was never good enough for Emily, and when Emily solves this case, Nick and the FBI will look like morons.
The FBI finally figure out that the body Emily uncovered is Dr. Shen. His brother tells them that he gave Emily the key to the storage room with Shen’s research. They find the audio tapes. They head to MIT and interview someone who knew Shen. Shen had complaints filed against him by students and was rumored to be involved with secret government research programs.
Emily breaks into Edgewater and pretends to be a patient. Another patient tells Emily that Charles is in a locked dudgeon at the end of the hall, but that Charles is really strong and he hurts people. The patient helps Emily steal the key to get to the so called dudgeon.
The FBI also tracks Charles to Edgewater and Gibbs and Nick get there just as Emily ends up battling Charles, but he won’t tell her who subject B was. Emily makes a run for it and Nick follows. Outside, they both end up holding one another at gunpoint. When Nick won’t let her go to save Flynn, Emily shoots him.