The scene opens in Gedawar Valley, Pakistan sixteen months ago. Dr. Horst Goebel leads a 16-year-old girl named Noura and a man into a place where there was a disaster. Children are lying dead in the streets. They approach a lake where Dr. Goble retrieves a cylinder. He tells the man and Noura that it is evidence. At Stokes Estate, Outside London present day, Sam climbs the walls. Inside, a security guard searches to find no one. Sam comes down the stairs and enters into a room. She gets on a computer and pulls up schematics of the estate. She makes her way to the Archive room and searches for Hourglass. An alarm is triggered and Sam finds the file. She takes it, but stops when she finds a file on her mother as well. She closes it when a man enters. She knocks him unconscious and another security guard comes in and tries to catch her. She fights and eventually kills him after being stabbed herself. She runs off and is seen on camera. She gets into her car and examines the damage.
Later, Aidan comes up and she gives him the file. It is covered in blood. He looks at the file and realizes that Hector Stokes had the file. He asks her what is wrong and Sam tells him that there was a report of her mother and how she was killed at a petrol station. Aidan asks why they would be looking for Sam all these years if the murder of her mother is connected. Simeran goes up to Keel and shows him the picture of Sam breaking into Stokes’ place. Elsewhere, a woman named Orla Fante gets a call from Hector and tells her that there is a problem. She tells him that she will be on the next plane. The next day, Jack Turner is shaving and Stephen is looking at Sam’s fake file. Jack cuts himself shaving and has a wild look in eyes. Stephen goes in to check on Sam and she and Eddie are not there. He is told that she and Eddie left early. At a stable, Sam feeds Eddie’s horse and he tells her that he comes every week. Sam says that his mother would be proud. Eddie snaps back and says that Sam didn’t know her mother. She tells him that she would be proud either way that he is taking care of something.
Stephen comes up and asks to speak to Sam. He tells her that she has some explaining to do. He says that the police found her fingerprints at Lewis’ place the night he died. She tells him that he wanted to talk to her about something about Goncourt. Stephen is shocked by this and Sam says that she would expect this from Jack and not him. He apologizes and says that he is paranoid. He says that Jack had something to do with Lewis’ death. He says that he is leaving tonight and asks for her to come with. At Jack’s place, Ian sees Jack leave and Zoe and Deacon tell him to get close. He puts a satellite on a building to hear in. Jack meets with Rahim Soomro, the Pakistan minister. He is told that Rahim is disappointed. Jack tells him that he has done a lot for him and Rahim says that the government has given the Chinese the bid. Jack says that it is Polyhedrus who is the problem. Jack has proof what Polyhedrus did to build the dam and that he better give him the bid. Back at Byzantium, Deacon says that Jack is planning to blackmail Polyhedrus. Zoe says that the company is huge and that Hector Stokes is the CEO of it. Deacon says that Jack has evidence and Ian says that he doesn’t really know where the case is anymore because the police are after him. Aidan says that Sam must have heard or saw something that would make Stokes want her dead. He tells her that she needs to remember.
Orla arrives and recognizes Sam. She asks what the task is and she is shown the picture of the Blank Faced Man. She tells Hector that she needs information. Natalie meets with Aidan at a train station. He shows her the file and she doesn’t recognize the watermark. Aidan says that Byzantium isn’t the only one with a mole. Natalie says that Aidan hasn’t told Sam who he really is. Sam gets back to the Turner’s to find Stephen in the room. She shows him the news article of Goebel drowning. Stephen tells her that he should have left a long time ago. They kiss. Bingham goes up to Stephen’s room and finds a folder of Sam’s fingerprints. Stephen meets with D.I. Everett and thanks him for the fingerprints. He asks what other services he covers and asks if he “takes care” of people. He tells him that Dave Ryder is the man who takes out people. He says that he can steer an investigation if he wants and Stephen tells him not to touch him. He leaves and it turns out, Stephen recorded the entire conversation.
Zoe and Ian pull up to Dave’s and Ian says that he has a fresh start now. Zoe gets a call from Andrew. She is told that an old friend wants to see her. She leaves Ian at the bar. Ian gets in and Dave says that he can’t be coming in there. Ian says that Tyrone framed him. Zoe gets home to find Orla there. Andrew leaves and Zoe asks her who she is. She tells Zoe that she is a private security contractor. She is there to help Sam. Zoe and her walk and she tells Zoe that she wants to talk to Sam without the Blank Faced Man knowing. Natalie meets with Edward Gillespie, Under Secretary for the Ministry of Defense. She is told that she is in line for George Ballard’s job. She shows him the files and says that it was used to target a Byzantium agent. They were found in Hector Stokes home. She tells him that George was looking into Hourglass before he died. Edward denies everything and Natalie dismisses herself. She is told to keep everything quiet. Dave Ryder takes Ian to his place to hide him and offers him a beer. He tells him not to open the door for anyone. Dave leaves and Ian starts searching. Sam meets with Aiden and he tells her that he is sorry that she lost their child. Sam says that she doesn’t forgive him and says that he doesn’t understand.
Ian continues to search through house and finds nothing. Sam goes to the home of the girl who was at the site sixteen months ago. She shows her face and it is burned. She tells her that the Polyhedrus killed everyone in the city to build the dam. At Dave’s, Ian manages to find the case. He opens it to find Dave standing there. He is shot and it is Tyrone who is there. Ian runs and is gets the upper hand on Tyrone. He is about to kill him when a girl screams. He leaves Tyrone on the stairwell and takes the black case. At Byzantium, Zoe tells the team that Polyhedrus planned to flood the land, but Gedawar Valley was in the way. A “natural disaster” happened and the city was killed with gas. Dr Hill and Goebel told the news that it was a freak accident. They were going to blow the whistle, but Jack got to them first. Deacon realizes that Polyhedrus killed 600 people and that they are working for a mass murderer. Ian gets in and shows the case. It is filled with rocks. Stephen gets into the police station and tells the front desk that he has an appointment with the Commander. In Keele’s office, Sam comes in and asks Keele why he wanted to see her. He shows her the article on Hector Stokes. He tells her that she should have come to him. He asks her why she didn’t trust him. She asks what he is going to do and he says that it is nothing. Sam says that he executes orders no matter what.
She walks and Natalie finds her. She tells Sam that they both are in great danger. She tells her that Aiden hasn’t told her who he really is and gives her a key with Aiden’s MI6 file inside. Aiden watches the exchange. Ian is upset and Deacon tells him that it is hard. Zoe says that the real case is still in the library. At the police station, Stephen gets into the Commander’s office, but finds Jack there. He tells him that he doesn’t betray family and Stephen says that he is crazy and that he is taking Eddie and leaving. Jack asks if he is taking Sam with him and calls her a tart that is getting paid to screw Stephen. At first Stephen doesn’t believe him and then Jack convinces him that she is trouble. Stephen says that Jack is not to hurt Sam. He promises. Bingham and Tyrone pick up the Everett and Bingham asks how Stephen got the file. Everett tries to lie his way out of it and Bingham and Tyrone kill him. Keele goes to meet with Hector and he is told that Jack is to be killed. Keele asks why Hector wants to do this so quickly and Hector asks him what he means. Stephen and Jack get home and Sam is called into Jack’s office. He offers her some tea and tells her that she is to be in the house for a long while. The episode ends.