At the warehouse, Claudia tries to pinpoint the transmission signal within the warehouse while Pete and Myka search the warehouse and Artie coordinates. Claudia confirms that the signal is coming from the art gallery and goes with Artie to investigate. Everyone meets there and finds nanites have infiltrates the system. Artie realizes that they emerged from the Van Gogh that sally temporarily took from them. Claudia warns that it will take her days to interface with their coding so Artie has Pete blast it with a Tesla rifle.
Tyler, running the nanites on remote, realizes that the agents have shut down them down. Sykes asks for a report and Tyler admits that he has the data he wants but hasn't decoded it yet.
Jane Lattimer arrives and demands a report. Claudia confirms that Sykes accessed File Atlas-66. It's for Regent use only and Myka suggests that Jane should tell them what it is. She refuses, insisting that the Regents already have a plan in place. When Myka turns to Pete for support, Pete agrees with his mother and then quickly slips away, and Myka reluctantly agrees to drop the matter. However, she goes after Pete and demands an explanation. He warns that arguing with Jane will get them nowhere and reveals that he has a hideaway within the warehouse, his Pete Cave. He then shows her his planning board showing everything he's been doing to work out Sykes' plan. Pete figures that Sykes wants to get the Collodi Bracelet back, and made a fortune in hedge funds ten years ago so that he could get the Bracelet back. The agents wonder who Sykes has working with them now.
Steve and Marcus Diamond go to see Sykes, who says he wants them to collect something important. Later, Steve talks to Sykes and insists that he just wants his job and his reputation back. Sykes points out that they both have been burned by the Regents, and he promises Steve that he'll get his job with the ATF back. Marcus arrives and tells them that Tyler has decrypted the first part of the file.
While the agents start profiling Marcus, Claudia arrives and tells them she's identified Tyler Struhl's electronic signature on the nanite programming. She's obtained an address from the Atlas-66 file, an address in Cheyenne, Wyoming. The agents go to check it out against Jane's orders and Claudia runs interference.
At the B&B, Jane and Adwin argue over how to proceed. He wants to inform more Regents of her plan, but she points out that Sykes has already tortured and kill several Regents. She considers the Ramati Bracelet and admits that Pete is on the front line and her decision could get him killed.
Pete and Myka arrive at the Cheyenne high school and Myka finds Helena, teaching a class. She confronts the renegade but Helena has no idea who she is really is. Pete arrives and tells her to freeze, and Helena faints. They wonder why Sykes wants her and Helena wakes up and asks why they want her. Myka asks for her driver's license and they confirm that she's listed as Emily Lake.
At the warehouse, Artie comes in with the dog and finds Claudia working on her laptop. She claims she's doing nothing unusual but Artie doesn't believe it. Claudia finally admits that she's playing computer games because there's nothing to do. He leaves and Claudia then brings up the Atlas file and tries to decrypt it. Artie comes back and catches her, and demands to know where Pete and Myka are.
Helena takes the agents to her apartment and greets her cat, Dickens. As she feeds the cat, Pete suspects that Helena is up to something. Myka isn't so sure and finds fake photos on the wall. She figures that the Regents put her into their version of the witness relocation program. Atlas 66 refers to the fact that Helena was born in 1866 and lived at Atlas House. Helena comes out with a knife and tries to threaten them, but Pete easily disarms her, proving Myka's point. As Helena insists that she's harmless, Pete gets a bad vibe and looks out the window. He sees Marcus getting out of a car in the street below.
Marcus enters the apartment and finds Pete waiting for him while Myka gets Helena away. Pete demands to know what Sykes wants but Marcus attacks him. The two men fight and fall through the window onto the fifth-floor balcony outside. Marcus ends up falling to his death in the struggle. He runs to the parking garage to find Myka and Helena, and discovers that Steve has taken Myka's Tesla and has them covered. Pete explains that Marcus is dead, but Marcus walks in, alive and well. He says that they're done, and Steve stuns Pete and Myka and then leaves with Helena and Marcus.
Artie calls Pete and Myka, waking them up. He warns them that they're in big trouble and they explain that they lost Emily Lake. Artie knows who Emily Lake is and complains that they disobeyed orders, but the agents say that Sykes would have captured Helena regardless and now they know he's involved. They tell Artie that Steve is working for Sykes, and Claudia insists that he must have been controlled. Artie doesn't believe it and warns that sometimes people make the wrong choices.
Marcus and Steve take Helena to a hangar and demand the truth, but she insists that she's Emily Lake. Steve assures Sykes that Helena believes what she's saying, but Marcus prepares to control her with Cecil B. DeMille's riding crop. However, Sykes says that it won't work because it controls actions, not minds, and that he trusts Steve. He agrees to leave Helena alone while Tyler decrypts the rest of the files and get the answers they want.
Back at the warehouse, Myka demands an explanation from Jane, who explains that they tried to find a way to give Helena a normal life while keeping her as a resource. Claudia finishes cracking the file and discovers information on the Janus Coin. The artifact allows the user to separate a person's mind and body. Artie plays a video showing how Adwin used the Janus Coin to separate Helena's past and future lives, giving her a new personality as Emily Lake. The agents wonder who they've been talking to via hologram, and Artie explains that Helena's memories are on the Janus Coin, stored in Elk Ridge, South Dakota. Jane tells them to get the coin and bring it back before Sykes gets it.
Tyler decrypts the Atlas-66 file and finds the information on the Janus Coin, including its location outside of the warehouse.
Pete, Myka, and Claudia go to a Valu-Mart with a special key that will open the vault. When they take their list of goods to the checkout lane, the attendant JoBeth goes to call the manager, Mr. Keeler. He is wearing a Regent pin and takes them to a hidden vault in the freezer. After removing a box, he leaves and they confirm that a holosphere is inside. They slide the Janus Coin back in and the sphere projects an image of Helena's personalized past memories. They bring her up to speed on what has happened to her body and ask her why Sykes would want her. Helena has no idea why Sykes would want them.
They report to Artie, who tells them to keep a low profile and bring Helena back. As Artie cuts off, Jane is worried that she's not comfortable conducting military operations when she was an elementary school teacher. She tells Artie that she was chosen for her insight into children, and then explains that the Collodi Bracelet hardens the heart of the wearer. Artie wonders if they didn't get to Sykes in time when he was a boy.
As the trio drives back, Pete says that he has an idea for how to protect the warehouse, but warns that Myka won't like it. He then pulls over and says that they have to destroy the Janus Coin. Myka argues that it would be murder but Pete insists that the Coin can be used against the warehouse. His partner refuses to destroy Helena, and Claudia activates the sphere to get her input. Helena tells Myka that she must destroy the Coin to protect the warehouse. Myka says that the price is too high, but Pete and Helena note that once the Coin is destroyed, Sykes will have no use for Emily and let her go. Pete promises to save Emily and thanks Helena for everything she's done. Helena tells Claudia that she'll regret being unable to see her destiny, but is sure that it will be a glorious one. She tells Myka to be brave and then looks up at the sky as Claudia shuts down the sphere.
Claudia removes the Coin and gives it to Pete, but walks away with Myka because neither one of them can watch. Pete takes the Coin and prepares to smash it, asking for forgiveness. However, Marcus and Steve step out, using Cecil DeMille's riding crop to immobilize him. As Steve goes to get the Coin, Myka returns and draws on Marcus. Steve explains that they found them by tracing her cell phone GPS. When Steve points out that Marcus can't die, Myka turns the gun on Steve but he's confident she won't shoot. Marcus uses the crop to force Pete to throw the rock at Myka, and Claudia grabs the Coin and runs. Steve catches up to her and tells her to give him the Coin. She refuses and dares him to shoot her.
Pete hears gunshots and tells Marcus that he's a dead man. Marcus admits that he is as Steve returns with the Coin. He tells Pete that he can come after them or help Claudia and Myka, and Claudia doesn't have much time. Pete helps Myka up and they go after Claudia. She's fine and tells them that Steve revealed that he is undercover as part of Jane's plan. She accepted his story and gave him the coin, and Steve apologizes for not being able to tell her. However, Sykes plans to wipe out the warehouse and everyone in it, and he's putting himself at risk because he couldn't protect his sister. Steve then gives her the directions to Sykes' location, fires the gun, and runs off. The address is Skybrook 3, a decommissioned airport hangar.
The agents contact Jane, who explains that Steve had worked undercover with the ATF and was the most plausible traitor. He was ordered to cooperate and help Sykes however he could, and then send a message. The agents head for the hangar.
Marcus brings in Helena and Sykes puts the coin in her hand. The memories flow back into her, and Sykes offers her a glass of water and says that it's a pleasure to meet her. He then thanks Steve for all of his help.
The agents break into the hangar and search the place. Pete finds something upstairs but tells Claudia to get back to the car. She realizes that something is wrong and ignores Pete's warning. Running up the stairs, Claudia finds Steve, dead. Myka calls Artie and confirms that the Regents will send someone to get their friend's body. She goes to Claudia and asks her to hack into the laptop and find Sykes, and Pete angrily asks how she can carry on as normal. Myka says that if she doesn't, she'll lose it and asks Pete to help. He goes to Claudia and promises to stay with Steve. Claudia goes to the laptop but determines that they wiped the hard drive and Steve's death was for nothing. Pete and Myka vow to find Sykes and get payback.
Tyler drives Helena and Sykes away and she notes that he killed Steve in cold blood. He points out that she's killed a lot more people than him and she says she'll be glad to add one more to her list. When she tries, Sykes immobilizes her with Cecil B. DeMille's riding crop. Helena asks what he wants and he explains that he needs her advice on how to unlock a particular lock. She has a book which reveals that she learned how to do it from her teacher, Catarunga.
Catarunga introduces Helena to Warehouse 12 and has her absorb the first thing she smells: apples. He explains that his job is to teach and solve puzzles. He's impressed by her stories, and Helena admits that they're nothing compared to the warehouse.
Helena promises that she'll die before she helps him, and Sykes says that she'll live or die at her choice, but she'll help him no matter what.
Artie puts away Steve's room and complains to Mrs. Fredericks that she didn't tell him that Steve was undercover. She says that the Regents are regrouping and that the warehouse always comes first. As she walks away, Artie remembers the watch that MacPherson gave him and brings up his old friend's room.
Later, Artie returns to the office where Pete, Myka, and Claudia are still in shock. When he asks if they're all right, Claudia walks away and Pete explains that Sykes made Steve's death look like an accident. There was a cigarette lighter on Steve's body, but Claudia points out that he didn't smoke. She removes a flash drive from the lighter and plays it. Steve tells them that he doesn't know what Sykes' end game is but he's made travel arrangements to Hong Kong. Also, he knows that Marcus looks worried when Sykes brings out a wooden box with a particular artifact. Before he signs off, Steve tells Claudia to keep the faith. Jane comes in and says that Steve has given them the final piece of the puzzle: the location of the ancient Regent sanctum.
As Pete and Myka fly to Hong Kong, Jane tells them that the Sanctum was shut down over a hundred years ago. Claudia checks the flight records and confirms that Sykes has already flown to Hong Kong with only two people. Jane has found a Regent ring from Warehouse 7 and Myka recognizes the symbol on it. It represents the Eye of Horus and Artie confirms that a set of roads form the Eye of Horus, centered on the city of Tai Po. Jane tries to talk to Claudia but she walks away. The Regent goes after her and admits that Claudia has every right to be angry, and Claudia points out that Jane sent Steve to his death. Jane explains that Steve volunteered but Claudia points out that the Regent is trying to fix her mistake and assuage her guilt. She snaps at Jane, saying that the Regents are cowards and Steve is worth of a thousand of them, and walks away.
The agents arrive and find a restaurant in the center of the city. Pete gets a major vibe and they figure that the restaurant is on top of the Sanctum. They enter the basement and Myka finds Helena's locket.
At the B&B, Leena hears a noise and goes to investigate. The patio door is open but when she closes it and turns around, she finds Marcus standing behind her.
Myka searches the basement, figuring Helena left the locket as a clue, and finds a pattern of a door opening on the floor. They find the Eye of Horus inscribed on the wall and push on it, and the door swings open. Beyond is a hallway which leads to a chamber containing a chessboard. Sykes is using the riding crop to control Helena into forcing Tyler to play the game. He's fastened beneath a blade, and three wrong moves means that the blade will descend and split open his skull. Tyler makes his move but loses and the blade descends, killing him. When Myka and Pete react, Sykes hears them and forces Helena to capture them at gunpoint. The agents have no choice but to surrender.
As they move Tyler's body, Helena explains that her mentor, Catarunga, built the chessboard as a lock to protect the Sanctum. Helena says that Catarunga never showed her the chess lock and she has no idea how to use it. Sykes forces Helena to place Myka in the chair.
Marcus puts a wooden case on the table and tells Leena that it's a gift from a former employer. She grabs a pitcher, slams Marcus in the head, and runs down the hallway. He recaptures her, but not before she sets off an alarm. At the warehouse, Claudia turns on the security feeds and they realize that Leena is in danger.
Pete asks Sykes what they're going to find, and Helena warns that it could be an artifact too dangerous to be revealed. Sykes doesn't care and tells them to make the move. Helena explains that with Tyler, she tried the King's Gambit. This time she suggests the Dragon Variant and Myka makes the first move. The board makes its own move in response, putting Myka. Helena gives Myka the next move and she's put into check again. Myka tells Helena that she is not going to die because Helena will figure out the puzzle and save her life.
Helena refuses to carry a gun, but Catarunga says that the Regents have set the rules. She insists that there's always an alternate to killing and Catarunga agrees, showing her a Tesla gun. He demonstrates on an agent and tells Helena that sometimes it's necessary to change the rules.
Helena tells Myka to make an illegal move with her pawn. After a moment's hesitation, Myka does so and takes the king, winning the game. The blade retracts and Myka is released. Sykes calls Marcus and tells him to do it. At the B&B, Marcus goes outside and pulls the cover off of Black Barty's Cannon. Jane and Artie watch on the security feed and Artie warns that the cannon could destroy the warehouse.
In Hong Kong, the Sanctum begins to shake.
Marcus fires the cannon and it streaks across the desert, glowing with energy. Inside, Jane clutches at the Remati Shackle as a force field forms around the warehouse, deflecting the cannonball. Artie discovers that Claudia has left and Jane warns that the barrier can't stop something that is already inside. They go to the periscope and spot an energy column at the far end of the warehouse.
At the Sanctum, a portal opens to the warehouse. Sykes forces Pete to stun Claudia and Myka and then goes through the portal, bringing Pete with him. He forces Pete to shut down the portal, trapping Helena and Myka at the other end. Jane realizes that activating the barrier trigged the emergency exit, and Sykes had to unlock both sides. She warns Sykes that he'll never get what he wants, and has Pete knock Artie down when Artie tries to grab a weapon. Sykes tells Jane that they're going to find the Collodi Bracelet and Pete will give it to him.
At the Sanctum, Helena apologizes as she resets the chessboard, saying Myka should have destroyed the Coin. Myka tells her to get off of her high horse and they go to work.
As they go through the warehouse, Sykes explains that the Collodi Bracelet is part of him and he can't live without it. He forces Pete to take Jane captive, and Jane says that she takes responsibility for failing him and wants to help him. She walks toward him and says that he must know deep down that he needs her help. Sykes refuses, saying that he wants her to feel the pain and loss that he felt. He forces Pete to hand him the bracelet and tells Marcus to kill Leena. He prepares an injection but Mrs. Frederic arrives and threatens him with the Japanese Medal. Marcus puts down the syringe and Mrs. Frederic explains that Marcus was a former Baltimore Police Detective who was shot in the chest three times. She says that she can use the Medal to inflict unending pain on him, but he warns that she doesn't know what will happen next.
Sykes puts on the Bracelet and stands up from his wheelchair. Artie tells him to get out now that he has what he wants, but Sykes says that it's only step one and he wants Jane to know what it feels like to have something she loves ripped away from her. He uses the crop to force Pete to put the gun to his head, but Myka and Helena arrive after reactivating the portal and shoot the crop out of his hand. He flees and a rope falls down. It's the rigging rope from the Marie Celeste and both Helena and Myka are caught in it until Artie frees them using neutralizer fluid.
Jane goes after Sykes but he disarms her and comes after her. She knocks him down with one punch and runs to the portal, but he comes after her.
Marcus comes after with Mrs. Frederic with a knife, but Claudia arrives and takes out Johann Maelzel's Metronome from the wooden case that Marcus brought with him. Sykes used it to keep Marcus alive, and Claudia stops it. She looks down at him and says that she's killing him for Steve as Marcus rots in a matter of seconds.
Jane goes through the portal to the Sanctum and Sykes tries to go after her. Pete tackles him but Sykes shakes him off and tries to enter the portal. Pete shuts it down and Jane tries to pull Sykes through, but he disintegrates, leaving the Collodi Bracelet in her hand. Pete contacts her on the Farnsworth and tells her that he loves her, and Jane says the same. The others catch up and Pete tells them what happened and then hugs Helena and thanks her for everything. Claudia calls to say that Marcus is dead and they're okay. However, Artie realizes that the barrier is still active despite the fact that it should have dissipated instantly.
Artie realizes that Sykes never tries to kill them as he threatened, and that he left his wheelchair behind. They pull it apart and confirm that it contains an artifact, a piece of masonry that absorbed the entire force of the London Blitz during World War II. The barrier is still up to contain the explosion and protect the world. Artie tries to neutralize it without success.
As Claudia and the others try to find a way to stop the bomb by going through the files, Claudia looks at the metronome. Mrs. Frederic says that she needs to give it back, but Claudia refuses. She says that she'll use it to bring Steve back.
Pete tries to destroy the masonry with a blow torch but nothing affects it. With 56 seconds left, they realize there's nothing they can do to stop the artifact bomb. However, Helena creates a miniature force field to protect Artie, Myka, and Pete. She explains that an anomaly in system let her reroute part of the barrier to protect them, but she had to do it from outside. Helena smiles at Myka and remembers the smell of apples, and then the bomb goes off. A fireball shoots through the warehouse and the trio can only watch as everything inside of the building is destroyed.
The shockwave hits the B&B. Mrs. Frederic is knocked down and withers and dies in a matter of seconds as the warehouse "dies."
The barrier fades away and they realize that Sykes' plan was to destroy the entire warehouse, and they've lost. Artie looks at MacPherson's watch and says that they haven't lost yet.