The episode begins with White Vincent narrating the significance of the number four, as it relates to seasons, phases of the earth, and his pursuit of the fourth clock. Elsewhere, Melanie Lynch explains the history of the locust to the messenger boy, how it was once seen as a plague from God on humans but now controlled by science. She states it represents that God's power now lies in the hands of man. The boy gives her a coded message from White Vincent, and she responds by crushing the locust she holds in her hand.
Meanwhile, Hank and Agent Riley leave his hotel discussing the revelation that his wife had been living with him under a false identity for years. Riley seems to think that she has more to do with the search for the clocks, possibly working alongside White Vincent. Hank is at a loss, saying that Laila was a complete fabrication and never existed. At the Modern Skeptic headquarters, Arron explains to Father Mickle that the clocks together provide a map to the true cross of Christ. He notes the significance of the conspiracy and the lengths to which people are going to keep it protected and to discover it.
Hank returns home, looking at a picture of 'Laila' before tearing apart their bedroom looking for clues that could shed some light on Anna Massey's background. He recalls her tending to a hummingbird feeder and discovers a false bottom. Back at the Modern Skeptic, Arron and Rachel debate 'Laila's background -- is she working for the Shepherds, who protect the Cross, or the Pyrates, who are hunting for it? Rachel suggests she fled to protect Hank, but Arron insists that her entire life was a lie. Hank interrupts, showing the two the key that he found in the bottomed out bird feeder. He tasks them to find out what the key will open.
White Vincent sits uncomfortably in a public park, still reeling from his injury, as the messenger boy approaches. He passes Vincent a note: "You lost the bird. You lost the treasure. Do you need rest or replacement? Please advise." He insists he is fine, telling the boy to convey the message that he does his best work while angry. The boy curiously touches Vincent's gunshot wound, Vincent recoiling in pain. He restates that he is Melanie's best shot at finding Laila.
The timeline flashes back to Sydney, Australia in 2007. Anna Massey, dressed in full nun clothing, goes to speak with a priest at a large Catholic church. He tells her he has done some digging into her past -- she is a former thief and drug addict, lying about her background in order to get accepted to church. She claims the church has been her salvation, and she would do anything to stay under its protection. The priest relates the significance of The Shepherds, and asking her to join the order. He gives her a box of her old belongings to cast in a fire, burning her past life and giving herself fully to God and The Shepherds.
Back in present day, Hank meets with Agent Riley to learn that a surveillance sweep for Laila has yielded nothing. Hank has been doing some digging of his own, remembering that Laila used to volunteer at a garden every week in the early mornings, significant since she hated mornings. The two stake out the part of the garden which Laila tended to, trying their best to look inconspicuous, when a man approaches and digs up a note. As they near him, the stranger recognizes Hank and makes a break for it. A chase ensues, and the man makes his way to a rooftop where he perches on a ledge. He tells Hank he has to stop searching for his wife, that a Shepherd keeps his secrets until the end. Before they can learn anymore, he jumps to his death.
Later, Riley and the police look over the man's body. The note in his pocket reads "352 irrelevant," and is written in Laila's handwriting. Back to 2007, the priest and Anna walk the boardwalk outside The 41 Trust fundraiser as he explains the significance of the Pyrates and their search for the relics. He gives her an assignment to go undercover to South America to look into a strange clinic run by the Pyrates. Anna is torn, seeing it as a return to her old life, but the priest insists that her actions are holy as she spies Melanie Lynch raising a glass at the fundraiser.
At the Modern Skeptic, Rachel relays that they have found the locksmith who made Laila's mystery key. As she tries unsuccessfully to call locations that utilize the locksmith, Arron and Paige enter with information on Laila's metro rail card. They find that she has taken regular trips to Flatbush every week for years, and Hank and Riley head to the area to look for buildings with corresponding locks. They come upon an apartment building where a neighbor recognizes Laila as a resident in one of the flats. They kick open the door to find an empty apartment. Hank again struggles to come to terms with Laila's second life, lying to him for years to come here and pray. He flips through her Bible, finding a photograph with Laila and a mystery Asian woman.
They return to the Modern Skeptic HQ to analyze the photograph, discovering that it was taken in Paraguay. Hank notes that they have never been to South America. Another flashback, this time to 2008 Paraguay, and Anna is walking the streets of Ascuncion with the woman from the photograph. The woman works at the Pyrate clinic, and Anna gushes over the chance to volunteer for such a fulfilling position. After the woman pledges to pull some strings to get her a job, the two pose for the photograph.
Later, Hank looks over the photograph as Father Mickle approaches with news that he spoke to a priest in Ascuncion who did not recognize Laila. He notes the mystery woman's armband is worn by public health workers, which could provide a clue to her background and why Laila was interested in her. Just then, Riley enters and states that the D.C. office just recorded Laila at Dulles airport only six hours earlier before disappearing, and they learn that one of the international flights during that time was to Paraguay.
Father Mickle speaks with Father Reggie to see if he has any insight into Laila. Reggie pleads ignorance, stating he only knows of the Shepherds but has never met one. Mickle conveys the "352 irrelevant" message, which Reggie again is clueless about, and it is revealed that White Vincent is seated just a few feet away eavesdropping. Vincent also hears that Hank went to Ascuncion, and Reggie again tells Mickle that The Shepherds should not be crossed.
In Ascuncion, Hank and Riley survey the area in which the photograph was taken, asking those nearby if they recognize either of the women. One local reveals that the armband is for volunteers at the Santa Marta Clinic, but that no one in the area trusts the clinic, dubbing it cursed. As they drive to the location, Riley wonders aloud why a clinic would be placed in such a remote area. The site appears abandoned, but the two move in for a closer look, finding a jeep with a still-warm hood.
Back at the Modern Skeptic, Rachel continues to look into Laila's past as Arron arrives. She makes a jealous remark about Arron spending time with Paige, and he realizes that she is angry. Rachel tells him she feels abandoned by Laila, and that she thought Arron would have lent a more sympathetic ear given his own family problems. He apologizes and promises that they will find Laila soon. She reveals that she has been looking into The 41 Trust, the charity which Laila and her mystery friend appeared to be working for in Paraguay.
At the Santa Marta clinic, Hank finds a volunteer armband near the entryway of the abandoned building. Back to 2008 at the clinic, Laila assists her friend with a sick malaria patient. She goes to refill her medication with one of the doctors, and feigns breaking down in tears over the emotional toll of the clinic. She pockets his security badge as the doctor consoles her. After leaving his office, Laila sneaks down into a secluded series of hallways, unlocking and entering the morgue with the security badge.
In present day, Hank and Riley travel the same series of hallways, finding nothing but empty medication bottles. Riley receives a call but has to leave the room for better reception, leaving Hank to explore on his own. As he rounds a corner, he is met by White Vincent, gun in hand. Vincent leads Hank further down a hallway, telling him that Laila is not here. He remarks that it is ironic: Hank came to the clinic to find Laila, but Laila came to the clinic and found Hank.
Meanwhile in New York, Arron and Rachel are in the lobby of The 41 Trust under the guise of a job interview. The human resources employee is puzzled when they ask about the Paraguay clinic, claiming they don't have one, but Rachel catches him off guard when she tells him that they did until 2008. He takes them elsewhere ostensibly to learn more about the Paraguay clinic, while Hank and Vincent explore the clinic's 'morgue.' Hank learns that the "morgue" is, in actuality, a site where researchers were continuing Nazi experiments relating to Project Zero Hour. Vincent claims he is unsure of why Laila was undercover at the clinic, and only knows what she found while there.
Back to 2008, Laila rummages through the "morgue" files, bagging several old film reels along with file folders on various patients/subjects, including 'Subject 352'. She photographs bodybags, praying quietly as she comes upon several live test subjects kept in cages. She breaks down at what she's seen, finally making it out to the open and meeting back up with her friend Emily. She tries to let on that the clinic is not what it seems to be, but is interrupted by the doctor calling her to tend to a patient. Emily returns to work as Laila flees the clinic. Suspicious, the doctor goes to the morgue to find that someone has stolen patient files and other items. He calls Lynch to advise, and she tells him to "Clean the mess."
In present day, White Vincent and Hank continue their exploration of the lab. Vincent finds the film reel for Subject 352, and notes that it is almost like fate in that he and Hank are discovering it together. Outside the clinic, Riley is shocked to learn that the person who rented the jeep was not Laila, but rather fits the description of White Vincent. She runs back inside as Hank and Vincent watch the film reel, which depicts Subject 352 as Hank's exact double.
At The 41 Trust, Arron and Rachel are greeted by Melanie Lynch, who inquires about their interest in Paraguay. Arron tells her they are writing a story on the Santa Marta Clinic, unique in that it was abandoned as opposed to the Trust's other clinics which are famous for their long legacies. Lynch notes that compassion is a commodity, available in a finite amount, and that the clinic failed both in terms of volunteers and as an investment for the Trust. It made more sense to utilize their resources elsewhere, and she asks why Modern Skeptic would be so interested in this.
Another flashback to 2008, as Anna/Laila has returned to Sydney to relay what she found to the priest, noting that the Trust murdered the 32 people she left behind when she took the file. She is uncomfortable that innocent people had to die for her to gain the information, stating that she is fine with sacrificing herself but not others. The priest again asserts the importance of the information, that it is key to stopping Zero Hour. He gives her the follow-up assignment to keep tabs on Subject 352, and gives her a flyer which advertises a promotional appearance for Hank Galliston.
Hank watches the film reel in shock, demanding that Vincent tell him who the man in the footage is. Vincent again claims he doesn't know, but encourages Hank to join him to hunt down Laila so that they can demand the answers together. He says they share a fate, and unveils a tattoo on his right forearm: "353." Just then, Riley rounds the corner, gun drawn. They exchange gunfire and Riley is clipped in the shoulder. As Vincent moves in for the kill, Hank breaks a wooden board over his head. He and Riley leave, laying low in the jungle outside as Vincent again calls for Hank to join him in his search for answers.
Laila meets once again with the priest in present day Sydney. He notes that with the clocks in their possession, the location of the Cross is safe. They repeat the same ritual of burning items from her past life, only this time the box is filled with Laila Galliston's things. Another priest with his back turned to the two asks if she is ready to throw away such a large part of her life, turning around to reveal Father Reggie. Laila insists she is ready to burn it all and casually tosses the box in the fire.
Back at the clinic, Vincent gives Hank one last chance to join him, calling him his brother and saying that if he walks away from this they will be brothers no more. Hank looks on as Riley slips out of consciousness from the blood loss. Back to Sydney, Laila prays for God's protection of the innocents, revealing that she kept one photograph of Hank after all.