Emily enters the tunnel and is hit with a tranquilizer dart from the person in the mask.
Emily awakens to find she’s locked in a dark room with Alice, who is unconscious. A voice over a speaker tell of how Emily was labeled as aggressive and not likely to be adopted as a child. But Emily switched the paperwork in her file, and was later adopted, while the person she switched files with ended up being Dr. Shen’s subject B.
Dr. Shen believed that children who survived early trauma could be turned into killer soldiers. Subject B was Logan Brandt, now known as Laurie Colson, the reporter working with Jack. Laurie says that she and Charles both killed Shen so that he couldn’t hurt them any more. Conrad Harlow was her partner. Laurie wanted revenge against Emily and Harlow hated Emily because she was the FBI agent closing in on him.
Laurie has Flynn back in the tank. She tells Emily to kill Alice or Flynn will drown. That’s when Nick finds Emily but he still believes she’s behind all of this. Alice wakes up and the they save Flynn but Nick holds Emily at gunpoint as they try and leave the tunnels. Then shots ring out. Nick gets Alice and Flynn to safety while Emily goes after the shooter.
When Nick gets Alice and Flynn to the car, he doubles back to find Emily. Emily follows Laurie/Logan into the woods. The two fight. Laurie tries to drown Emily, then Emily turns the tables but refuses to drown Laurie. Then Laurie hits Emily in her gunshot wound and Emily has just enough strength to hold Laurie under the water until she’s dead.
Bleeding, Emily gets up and finds Nick has been shot just as the FBI tracks Nick’s cell phone and gets to the cabin and arrests her.
Agent Crown sends Gibbs to check out an old employee of Barrett House who has some files in her attic. Gibbs says there are files to help them track down the other victims of Dr. Shen.
Emily is exonerated of all charges as the FBI and Boston PD realize that Logan/Laurie was behind the abductions and the murder.
Nick apologizes to Emily for not believing in her and she accepts. They both agree that they’ve changed since her abduction. Emily says that Alice is good for him and he tells Emily that Alice is pregnant. Emily congratulates him.
Later, the entire family, including Emily, Warren, and Jack, join Nick and Alice for Flynn’s birthday. Everyone is happy. Detective Gibbs is there and subtly hits on Emily once she gets settled. She says she plans to go back to the FBI once she’s taken some time off.
But in the kitchen, when the dishwasher begins to leak, Emily has a panic attack cleaning up the water, and she is shocked at the vision of herself drowning someone.