As Margrove requested, Peter meets him in the tunnels. He tells Peter the Order of Moriah hired him to get them to the Well of Souls but now he wants to stop them from destroying the foundation stone beneath the Dome of the Rock, which is sure to bring about Armageddon. He was only ever interested in the Temple Treasures, which Margrove tells him are behind a two-foot wall in a passageway called Warren’s Shaft. Afterwards, Peter rushes to the scene of Golan’s accident, but he’s too late: Golan is already dead. However, next to his body, the name “Rebecca” is scrawled in blood on the ground. Peter runs inside the psychiatric institute and barges into Gregory Donaldson’s room demanding to know who Rebecca is but Gregory is out of it again and the orderlies drag Peter away.
Lynn is blindfolded in the back seat of an SUV that’s driving through the desert. Next to her is Liat, who is texting with Ridell, giving her updates as they go. Eventually Lynn manages to knock out Liat, shoot the driver, grab Liat’s cell phone and free herself.
Peter returns to Itay’s apartment to see Emma. She notices that Peter has sandstone on his shirt, which she explains doesn’t make sense: there wouldn’t be sandstone in the tunnels because it doesn’t work with water, which makes something click in Peter’s head. Both Margrove and Donaldson said you have to follow the water, so Peter goes to see Udi, Golan’s significant other, who is a geologist specializing in the underground waterways. Udi explains that if a dam at Beit-Zait above the city were destroyed, half the city would be flooded through the aquifers. The only way to prevent that is to enact the “Armageddon Protocol,” which engages a set of automated steel doors that seals off escape routes.
Shem secretly meets with Avram and hands him a knife. If Avram wants to stop Rabbi Lev and his men, he needs to kill Joshua.
As Emma is walking, a car pulls up alongside her. It’s Margrove. She gets in and he asks if Peter bought her story about Warren’s Shaft and the sandstone. She says he should be finding out about the Armageddon Protocol right now. Then she says, “Let’s go get our treasure.”
While Joshua is getting fitted for high priest robes, he tells Billingham that he has served his purpose and orders him to go. While relaying this shocking exchange to Faye, Billingham decides that Satan has taken hold of the boy so they must continue on their path without him. Faye reminds Billingham that she carried and raised those boys and won’t destroy this Joshua, too. Billingham gets so worked up that he starts choking on the nuts he has been eating but Faye does nothing to help him. Within moments he takes his last breath while she looks on, the job of stopping Billingham neatly done for her.
Lynn flags down a guy riding a motorbike and gets a ride back to the consulate. Ambassador Ridell arrives at the same time with Israeli Defense Minister Krugman, so Lynn ducks out of sight.
Peter drives to the dam just outside the city where he sees Shem. He follows Shem down into the bowels of the dam, where he finds Billingham’s books, which were clearly just shells to hide something within them, strewn all over the place. Then he sees that the base of the dam is rigged with explosives the size of the holes in the books. They have less than twenty minutes before the explosives detonate but Peter is unable to defuse it because it’s failsafe. When Lynn calls Peter, he tells her she needs to get someone to enact the Armageddon Protocol. She tells him Defense Minister Krugman is in Ambassador Ridell’s office but she needs to find out what side he’s on. Peter tells Shem that even if the protocol is engaged, it won’t save the Dome of the Rock because the Well of Souls is covered in sandstone, which isn’t strong enough to hold up the foundation stone above it. Their only hope may be to get to Warren’s Shaft and see if they can divert the water down there.
Meanwhile, devoted followers circle around an altar at the Temple of Absalom where Joshua, dressed in his robes, is getting ready to sacrifice the red calf. Rabbi Lev leads the ceremony while Avram watches and waits for his moment.
And deep in the tunnels beneath the apartment that John Donaldson once occupied in the Sisters of Dinah convent, Margrove shows Emma the Temple Treasures.
Lynn sneaks into Ridell’s office. When the Defense Minister comes in, Lynn comes up behind him and puts a letter opener to his neck. She tells the Defense Minister that a bomb is about to blow up the dam and he either already knows that or will engage the Armageddon Protocol. Downstairs, Phil tips off Ridell that he’s seen Lynn on the security cameras so Ridell and her armed men burst into her office. Ridell tells the Defense Minister that Lynn has been suffering from delusions but Lynn convinces Krugman that he has nothing to lose by enacting the Armageddon Protocol. Despite Ridell’s protests, he makes the call.
In the Well of Souls, Peter and Shem take sledgehammers to the wall separating them from Warren’s Shaft. They reach the shaft but it has a false floor. As Peter frantically tries to break through it, they hear the sound of far off explosions.
When the steel doors move into place, Margrove says to Emma, “The end of their world, the beginning of ours” and she replies, “Thank you, Peter Connelly.” Emma then says that her father was right about everything. It suddenly dawns on Margrove that Emma is the daughter of his old colleague John Donaldson.
When the dam explodes, it sends everyone at the Temple of Absalom scattering to get a better look at the devastation across the valley they know is coming. Red is left behind so Avram quickly sneaks off with her. When they see that the Temple Mount is not crumbling, Rabbi Lev, Faye and Joshua return to the altar to continue with the sacrifice but the calf is gone.
Shem and Peter cling to a ladder in the shaft as the water rushes in. As they hoped, the water is diverted down into the newly opened shaft.
Lynn and the Defense Minister look out over the Old City, which stands unchanged, while Ridell is escorted out of the building in handcuffs. Later, Peter has made his way back to the consulate. Lynn has a lot of work to do figuring out how many others were involved but she’ll be doing that without Peter. When he goes back to his office to clear out his belongings, he notices Gregory Donaldson’s file on his desk. Inside he sees the name Rebecca Donaldson and suddenly realizes who she is. He drives to the Sisters of Dinah convent and goes down tunnel from John Donaldson’s old room. There he finds Margrove’s lifeless body and Emma—aka Rebecca Donaldson—standing nearby. She says she’s been waiting for him. Peter asks her if this was all about revenge but she says it was about bringing the man who took everything from her to justice. At age fifteen, when she learned the story of what happened to her family, she became Emma Wilson, enrolled in University of Pennsylvania and took all of Margrove’s classes. She seduced him and he told her about the people who were paying him to dig where no one should be digging. She knew all about the Order of Moriah from her father’s crazy rants. Enacting the Armageddon Protocol was the only way to stop them. Margrove was able to target Peter as someone who could accomplish that for them. So with Emma’s help, they were able to draw in Peter by exploiting the death of his daughter. But she never counted on falling in love with Peter. Now that it’s all over, she says, they can be together. But he informs her that soon the place will be swarming with police because ultimately she did a lot of bad things including killing Golan. He just came to say goodbye. As the authorities storm the tunnel led by Lynn, Peter walks back into the light.
That night, Lynn goes to see Peter in his hotel room. She says Emma didn’t go down easily but they have her in custody along with Rabbi Lev, Joshua and Faye. She asks him where he’s going to go now. He says he was thinking of asking his boss for a transfer far, far away and thanks her for being his friend.
Two weeks later, Avram has given up his orthodox garb and his faith. He has brought Red to a remote cattle ranch. He gives the rancher instructions for her care: no milk, no meat, let her die a natural death and if anyone asks, tell them she’s blemished. Then Avram leaves her, satisfied that she is safe, and walks toward an unknown future.