A voiceover explains the significance of the number six: the number of evil. Sometimes a person must ally himself with his foe in order to move forward. White Vincent explores the wreckage of Nazi submarine where Hank found Sturm's frozen body. He returns to his ship with the submarine's log book.
At the FBI office, Riley learns that Hank spoke with Laila on the phone to set up the meet via a wiretap on his phone. Riley is perturbed that Hank did not tell her about this, and sets several agents to survey the meeting area. Laila is at the park, awaiting Hank's arrival, but spots several people in the crowd watching her. She is approached by Arron, disguised as a jogger in a black hooded sweatshirt. He tells her Hank doesn't trust her not to double cross him, and tells her to get on a bus which will take her to the meet up location. She gets on the bus with agents running far behind, and sees Rachel is already on board. Rachel tells her to switch coats, taking Laila's umbrella and telling her that a note will be posted underneath the bus bench at the next stop. Laila attempts to apologize for her deceit, but Rachel isn't having it. As Rachel gets off the bus with Laila's jacket and umbrella, operatives sent by Father Reggie follow her under the notion that they are tailing Laila. She ditches the jacket and umbrella, and the operatives phone Reggie to tell him they lost track of Laila.
At the next stop, Laila finds Hank's message with a meeting spot: the bridge where Hank proposed to her. The two share a tenuous moment, as Hank tells her he could have proposed anywhere and she would have accepted, because it was just a job for her. Laila professes that what began as an assignment became much more. She tearfully claims she fell in love with him. Hank tells her to stop defending herself and to explain her actions. The two walk and talk, and it appears that Laila is almost as in the dark as Hank: she was assigned to protect him, but isn't sure from what or whom, nor does she understand the background of Subject 352. She follows orders from The Shepherds with blind faith. Hank tells her he is willing to trade his "one" clock for real answers, or else he will talk to the Pyrates. Laila claims the Pyrates are dangerous, intent on invoking the hand of God to bring about the end of times. He tells her to deliver the message and leaves.
In the Modern Skeptic office, Hank relays how the meeting went to Rachel and Arron. Arron is still hung up on how Hank could be the father of the 70 year old Erik Haas, joking that the only explanation is time travel or reincarnation. Rachel chides him after Hank retreats to his office. Rachel and Arron have meanwhile been looking at the last clock Erik found, finding a Latin inscription on the bottom: "Without twelve there is none. With a dozen, there is one, through which divine light shines and reveals the beginning of time."
Back in the arctic, Vincent looks through the log book finding that it is written in the same mysterious code that Lynch has been using. He calls her to get the services of a demotic translator to decipher the log, hopefully revealing a clue as to where Sturm could have stashed the True Cross. Lynch is at one of The 41 Trust's medical clinics along with the messenger boy. She apologizes to him for keeping him in the dark, hinting that there is a much bigger plan for him.
Back in New York, Riley confronts Hank over the meeting with Laila, angry that he would keep her out of the loop when she is also looking for answers about her husband's death. She thinks he did not include her because it is too personal, that he is still clinging to the past and hoping that some part of his life with Laila is real. He denies this, and she points out that he is still wearing his wedding ring. She warns him that if he sets up another meeting without her that he will be arrested for obstruction.
Laila's prayers at the church in Sydney are interrupted by Father Reggie, who informs her that given her actions he will be taking over negotiations with Hank. He thinks that she still has feelings for Hank, that things are too personal, and tells her that by destroying the bridges behind us we can then move forward. Father Mark interjects, as The Shepherds have learned that The Pyrates have found Sturm's submarine. Mark also reveals that Hank's negotiation is a bluff -- he has not just one clock, but all the remaining clocks. Reggie sees no choice but to take them by force if necessary, and kill Hank to avoid his further involvement. Mark seems shocked to hear this.
That evening in New York, Riley arrives at the Modern Skeptic office having just gotten Hank's message to meet. He informs her of his intent to meet up with Laila again, and agrees she was right that it was unfair to keep her out of it before. To show his commitment, Hank has removed his wedding ring. Hank tells her that looking at Laila was like looking at a stranger -- he owes nothing to her. The two share a drink as they talk about future plans after the investigation wraps up. Riley wants to return to social work, seeing the FBI work as just a means to learning the truth about her husband's death. Hank is less sure about his future.
Vincent meets with the demotic translator, who is amazed at the log books that have been found. He tells Vincent that it shouldn't take more than eight hours to translate. When he inquires where the texts were found, Vincent tells him to translate first and questions will be answered later. Meanwhile, Hank receives a call from Father Reggie to arrange the exchange, and he reveals that he knows Hank has all the clocks. Hank, Arron and Rachel set up a decoy to ditch any potential tails -- Hank and Arron will arrange the distraction while Rachel escapes with the clocks. Unfortunately, after Arron successfully ditches his two followers, Hank is stopped by Reggie who reveals that he already has Rachel.
Later, Father Reggie takes Rachel and Hank to a secluded mansion, leaving her outside while he takes Hank into the house. Hooded figures line the hallways, following Reggie and Hank to a room where the twelve clocks are being arranged. Reggie reveals that Hank's destiny has been tied to the cross, and asks that he work on the puzzles inside the clocks to once and for all find the answers he's looking for. Reggie excuses himself for a phone call. One of his operatives is on board the ship with White Vincent and the translator, and Reggie tells him to find out how much of the demotic text has been deciphered. The operative goes to the translator's room under the guise of looking for cleaning supplies, only to be interrupted by Vincent who has learned his identity. A knife fight breaks out, and Vincent gets the better of the Shepherd while the translator looks on in horror.
Laila tries to get answers about Hank's past from Father Mark. She asks about flight 71, the wreck that cost Riley's husband his life which Laila was supposed to be aboard. She tells him that what caused her to miss the flight was that her cab was broadsided by a bus. After crawling out of the wreckage, she claims to have seen a divine message on the bus' route display: "857" becoming "352." At the mansion, Hank goes over the clues of the twelve clocks, reciting the Latin inscription aloud. He and Reggie are interrupted by the arrival of Mark and Laila. Reggie objects, but Laila reaffirms her commitment to The Shepherds cause. She attempts to help Hank decipher the clues, which seem to revolve around glass disks that were found inside each clock.
At the FBI office, Arron tries to get answers about the disappearance of Hank and Rachel. Paige brings information about the license plates getting caught on camera and the last location of the car. Meanwhile, Hank and Laila realize that each glass disk has a unique etching, and that stacked together they reveal a full map of the world. Hank marks the locations where each of the twelve apostles were located, theorizing that this in conjunction with the map could point to a more specific location. Together, the points on the map form a perfect circle, and at the center of the circle is Strasbourg.
Hank tells him that with his end of the bargain complete, it's time for Reggie to reveal the truth about his background. As the FBI closes in, Reggie tells Hank that his life is a direct result of Project Zero Hour. The project's purpose was to harness the power of the cross to bring about the end of days; the cross may appear to be nothing but wood, but Reggie claims that inside is the power of a thousand atomic bombs and Hank is the detonator. They are interrupted by news that the FBI is getting close, and Reggie excuses himself. As he leaves, he whispers to Father Mark that he must kill Hank. Mark raises a gun on Hank, asking God's forgiveness, but Laila lunges at him as he fires. The bullet shatters the glass disks. She grabs the gun and shoots Mark, telling Hank to come with her.
Vincent calls Lynch to tell her that the charts have been translated, and she tells him to tie up the loose ends. The messenger boy interjects, and she continues a Bible lesson as the exit the medical clinic to reveal they are in a desert. Back on the boat, Hank gives the translator the option of a quick death by gunshot or jump into the freezing ocean water.
Rachel is held captive in the basement of the mansion, kicking the door open just as the FBI arrive on the scene. Elsewhere, Hank and Laila arrive in the city and Hank turns his cell phone on to allow the FBI to trace his location. Laila implores Hank to help her find and destroy the cross, saying that if Jesus knew that people were dying to discover its location he would want it destroyed himself. Hank is doubtful after all the lies she has fed him. He asks her to tell the truth about the night he proposed: she claimed at the time that she left to tell her mother the good news, but Hank asks if she was actually contacting The Shepherds to relay the success of her operation. She admits that she did just that.
The FBI rolls up on Grand Central terminal to find Hank's cell phone taped to a lightpost, along with an apology note. Hank and Laila drive away together.