At the warehouse, Claudia and Artie try to pinpoint a signal within the warehouse while Pete and Myka search the aisles. Claudia finally pinpoints the signal near the art gallery and goes with Artie to investigate it. They discover that nanites are loose in the warehouse and are responsible for the recent computer glitches. Artie realizes that Sally slipped them in on the Van Gogh, and Claudia confirms that they’re downloading encrypted data. Since she can’t interface with the nanites’ programming, Artie has Pete fry them with his Tesla.
Tyler Struhl loses contact with the nanites and Walter Sykes asks what is happening. He tells his employer that he got what they needed and now he has to decrypt the data.
Jane Lattimer examines the nanite debris and has Claudia determine what they were downloading. She finds a file named Atlas-66 and Jane says that it’s for Regent use only. Myka suggests that Jane should tell them what is in the file, but Jane insists that the Regents have a plan, overriding Myka’s objections. When Myka turns to Pete, he sides with his mother and says that they have to respect her because she’s wearing the Remati Shackle. Jane goes to see Adwin while Pete goes off. Myka follows him and he explains that he knew Myka would follow him. He reveals that he has a secret “Pete Cave” and that he’s worked out all of the connections between Sykes, Aquino, Stukowski, and the mysterious Marcus Diamond. Sykes has made millions in hedge funds and then vanished ten years ago. And all of his minions have been killed.
Marcus meets with Sykes at a hangar and tells him to stay close along with his new partner: Steve Jinks. Sykes talks to Steve privately and assures him that he’ll be able to restore his life and his reputation once they take down the Regents and destroy Warehouse 13. Once Sykes has the Collodi Bracelet, he promises Steve that he can do whatever he wants.
Myka suggests that they profile Marcus. Claudia arrives and tells them that she’s confirmed that Tyler was responsible for the nanite programming. She’s obtained the name of Lincoln High School in Cheyenne, Wyoming, from the Regent files and the agents go to investigate.
At the B&B, Adwin says that they should eliminate Sykes immediately, but Jane insists that her current plan will reveal what Sykes’ plan is and that they need to know it. She admits that she could lose Pete as well as the warehouse.
At Lincoln High School, Pete and Myka search the high school. Myka finds what Sykes wants: Helena. She’s apparently posing as a literature teacher, and Myka goes to talk to her. However, Helena has no idea who she is and is now speaking with an American accent. When Pete charges in with his Tesla, Helena momentarily faints in shock. They ask to see her driver’s license and determine that she is now going under the name Emily Lake.
At the warehouse, Artie finds Claudia working on her laptop. She claims that she’s playing computer games to relax, but he quickly catches her deciphering the Atlas-66 file against orders.
Helena goes to her fifth-floor apartment with the agents and feeds her cat, Dickens. They find fake photos of “Emily Lake” on the wall and conclude that she’s in the Regents’ equivalent of a witness relocation program. Myka realizes that Atlas-66 refers to 1866, the year that Helena was born, and Atlas House was where she was born. They figure they need to get her safe before Sykes finds her. Helena comes out with a knife and Pete easily disarms her, and then spots Marcus pulling up outside.
When Marcus comes in, Pete gets the drop on him and says that he just missed Helena. Marcus attacks him and after a brief struggle, Marcus plummets off the balcony to his death. Pete goes to the parking garage and discovers that Steve has captured Helena and Myka. Marcus casually walks in, unharmed, and Steve stuns Pete and Myka and leaves with Helena.
Artie calls the agents, waking them up, and they bring him up to speed on Helena. Myka points out that Sykes would have gotten Helena whether they intervened or not, and that Steve is working for Sykes. Claudia gets the news and insists that Steve is being forced against his will, but Artie says that he went along voluntarily and that he made his own choices, even the wrong ones.
At the hangar, Marcus tries to interrogate Helena but she insists that she’s Emily Lake. Steve confirms that she believes she’s telling the truth, and Marcus prepares to use Cecil B. DeMille’s riding crop. Sykes warns that it can control actions but not minds, and says that they’ll leave Helena alone while Tyler decrypts the file and gets the answers they need.
Back at the warehouse, Artie and Jane explain that Adwin used an artifact, the Janus Coin, to separate Helena’s past memories from her future life. Her memories were stored on a sphere, which is what they interacted on earlier. Meanwhile, Tyler decrypts the rest of Atlas-66 and learns the location of the Janus Coin.
Myka, Claudia, and Pete go to a Valu-Mart in Elk Ridge, South Dakota, with the vault holding the Janus Coin. They have a special shopping list which Myka realizes were used in Egyptian burial vaults. The manager, Mr. Keefer, takes them to a secret vault in the freezer. They give him the key provided by Jane and he gives them the sphere with Helena’s memories. Claudia removes and reinserts the Janus Key, activating it and projecting an image of the “real” Helena. They bring her up to speed but Helena doesn’t know why Sykes would want her.
Artie orders them to bring Helena back to the warehouse. Once he signs off, Jane admits that she’s not good with military maneuvers and that she was selected for her expertise with children as a schoolteacher. She tells Artie that the downside to the Collodi Bracelet is that it plants a seed of darkness in the soul and creates an insatiable longing, hardening the wearer’s heart. Artie wonders if they didn’t remove it from young Walter in time.
As the agents drive back with the sphere, Pete has an idea for protecting the warehouse. He goes off-road into the woods and then tells Myka and Claudia that they have to destroy the Janus Coin. Myka says that it would be murder, but Pete insists that they’re at war and have to deal with reality. Claudia goes back to the car while Myka refuses to go along. However, Claudia returns with the sphere and activates it so they can get Helena’s input. Helena agrees with Pete’s decision despite the fact it will cost her her life. Pete points out that Emily Lake will be safe once Sykes realizes that she’s harmless without Helena’s memories. Helena assures Claudia that her destiny will be a glorious one. Helena then turns to Myka and tells her to be brave. Claudia removes the Coin and gives it to Pete, and the women walk away rather than watch their friend’s death.
Pete picks up a rock to smash the coin, asking for forgiveness, but Marcus arrives and uses DeMille’s riding crop to immobilize him. Steve is with him and steps forward to get the Coin, explaining that he traced Claudia’s cell phone. Claudia and Myka arrives and Claudia accuses him of being a traitor. Myka threatens to shoot Steve but he doesn’t think that she will. Marcus forces Pete to throw the rock, stunning Myka, while Claudia grabs the coin and runs. Steve goes after her and finally catches her. He demands at gunpoint for her to give him the Coin, and tells Claudia that there are things she doesn’t know about Jane and the Regents. She refuses and dares Steve to shoot her.
Pete and Marcus hear gunshots and Steve returns with the coin. They free Pete and Steve tells him that he’ll have to hurry if he wants to help Claudia. The two men leave and Pete picks up Myka and goes after Claudia. She’s unharmed and tells them that she gave Steve the Coin. He’s been working undercover as part of Jane’s plan to infiltrate Sykes’ organization and learn of his plan to destroy the warehouse. Steve has slipped Claudia a piece of paper with the words “Skybrook 3.” They confirm that it’s a decommissioned airplane hangar and depart. En route, they contact Artie and Jane, and Jane explains that Steve had worked undercover with the ATF and volunteered to go after Sykes, and he was under orders to assist Sykes to convince him he was a traitor.
Steve and Marcus return to the hangar and give Sykes the Coin. They bring in Helena and give her the Coin, and she regains her memories. Sykes introduces himself and offers her a glass of water, and then thanks Steve for his help.
The trio arrives at the hangar and start searching the place, only to discover that Sykes has escaped. Pete comes down and begs Claudia to stay where she is, but she realizes that something is wrong and runs upstairs. Steve is there, dead of an apparent heart attack. They call Artie who assures them that the Regents will send someone to collect the body. Myka asks Claudia to hack the laptop that Sykes left behind, and Pete wonders how she can ignore what happened to Steve. His partner says that if she doesn’t focus on Sykes, she’ll lose it. Claudia confirms that the hard drive has been wiped and Steve died for nothing, and the agents vow to get payback on Sykes.
As Tyler drives Sykes and Helena away, she points out that he murdered Steve. Sykes notes that she has murdered more people than he has and dares Helena to try and kill him. When she does, he immobilizes her with the riding crop, and then explains that he needs her to decipher a lock created by her mentor, Catarunga.
In 1989 at Warehouse 12, Helena arrives for her first day on assignment and smells apples. Catarunga says that it’s from the warehouse and must like her, and says that Warehouse 12 is more than just a building. His job is to teach and to create and solve puzzles. Catarunga is impressed by her imagination from the stories that he’s read, and tells her that there is always more to learn.
Helena vows that she’ll die before she helps Sykes, and he tells her that she’ll help him and whether she dies is up to her.
Artie seals up Steve’s room as Mrs. Frederic arrives. She tries to assure him that it wasn’t his fault that Steve died, but Artie insists that Steve was his responsibility. As she tells him that the warehouse always endures, Artie remembers the watch that MacPherson left him and his old friend saying that he would need it. He then brings up MacPherson’s quarters and goes inside. He then goes back to the office and asks if the others are okay. Claudia walks away without a word while Pete shows Artie a cigarette lighter they found on Steve’s body. However, Claudia realizes that it’s a clue and finds a flash drive inside. It has a video file of Steve leaving a message in the eventuality of his death. All he was able to find out that Sykes is heading for Hong Kong and that he has an artifact that makes Marcus nervous. Before he signs off, Steve tells Claudia to keep the faith. Jane comes in and tells them that the Regent Sanctum is located in Hong Kong.
Pete and Myka fly to Hong Kong while Jane explains that all information on the Sanctum was purged from the files. It was only a meeting place and Artie wonders why Sykes wants it. Claudia confirms that Sykes purchased three tickets, meaning either Tyler, Marcus, or Helena stayed behind. Jane has found a ring belonging to the Sanctum and Myka realizes the symbol on it represents an eye, as in the Eye of Horus. Artie checks a map of China and finds a pattern of roads centered on Tai Po that form the symbol. As Jane signs off, Claudia walks away and the Regent goes after her. Claudia points out that Jane was responsible for Steve dying alone, and that Jane’s plan was about making up for her own guilt for making Sykes. Jane refuses to discuss the matter and Claudia calls her and the Regents coward. She says that Steve was worth a thousand of them and walks away.
In Hong Kong, Pete and Myka find a restaurant at the intersection of roads. They check out the basement and Myka finds Helena’s locket and realizes that her friend left them a clue.
At the B&B, Leena is working when she hears someone break in. She goes to investigate and Marcus captures her.
The agents search the basement and find a hidden panel with the Eye of Horus inscribed on it. They open the panel and go into a chamber which holds a stone chessboard. Tyler is strapped to a chair and Sykes is controlling Helena to force his hacker to make a move on the board. Helena warns that she doesn’t know the correct move to make, but Sykes forces Tyler to play and a blade descends, killing him. Sykes hears Pete and Myka react and forces Helena to shoot at them. They have no choice but to surrender and Sykes explains that the chess lock was created by Catarunga. If someone wins the game, the door opens. Catarunga designed the lock when the Regents shut down the Sanctum, and Sykes figures that Helena knows how to solve the lock. Helena says that she doesn’t know how to open it, and Sykes has her put Myka into the chair. The board and the blade reset.
Myka puts down a box with a ticking noise coming from it and says it’s a gift from a former employer. She hits him over the head with a pitcher and runs, but Marcus catches up to her. Before he can stop her, she activates a hidden alarm. At the warehouse, Artie realizes that something is wrong. Claudia brings up the security feeds and they realize that Leena is in danger.
Helena warns Sykes that they may find an artifact too dangerous to be revealed, but Sykes tells Helena to open the lock. She suggest a new gambit, the Dragon’s Variant, and has Helena makes the first move. When she does so, the board moves its piece in response, putting Myka into check. Helena gives Myka the next move and she’s put into check again. Helena doesn’t know what to do but Myka says that she has faith in her friend and knows she’ll save her life.
Helena complains to Catarunga that she doesn’t want to carry a gun. He points out that it’s the Regents’ orders that all Warehouse agents must carry a firearm. Helena argues that there is always an alternative to killing and her mentor agrees. Agent Mcshane comes in and Catarunga stuns him with a Tesla, and says that there’s always a way to change the rules.
Helena tells Myka to make an illegal move with her pawn, capturing the king. The blade resets and Myka is freed. Sykes calls Marcus and tells him to do it. At the B&B, Marcus goes outside and unveils a canon in the back of his trunk. Artie realizes that it’s Black Barty’s Cannon and Jane activates the Remati Shackle. Marcus fires the cannon and the cannonball smashes into the forcefield that springs up to protect Warehouse 13. Jane warns that once the barrier is up, no one can get in or out. Artie discovers that Claudia has already left and Jane warns that the barrier can’t stop something that is already inside. They go out into the warehouse and see a massive energy discharge at the far end.
The Sanctum shakes and a portal opens up.
Artie and Jane go to the energy discharge and discover that it’s the other end of a portal.
Syke forces Pete to stun Helena and Myka and then goes through the portal. He brings the agent through with him and forces Pete to shut down the portal before Myka and Helena can follow them. Jane realizes that Sykes had to initiate the barrier to open the portal at one end and unlock it at the other end. When Artie tries to grab an artifact weapon, Sykes has Pete pistol-whip him. He then tells Jane that she’ll watch her son give him the Collodi Bracelet.
At the Sanctum, Helena points out that Myka should have destroyed the Coin as soon as she had it. Myka tells her to get off her cross and help her figure it out.
As they go to the shelf with the Bracelet, Jane warns that there are consequences to using it. Sykes insists that he has an overwhelming need for it and Artie warns that it darkens the soul of the wearer. He admits that they didn’t get to Sykes soon enough, and Jane says that they can still try to save him. She appeals to Sykes but he says he wants her to feel the guilt and pain that he went through. Sykes then compels Pete to hand him the Collodi Bracelet. Once he has it, Sykes tells Marcus to kill Leena.
Marcus prepares to give Leena an injection of a heart attack-inducing drug. Mrs. Frederic arrives with the drowning medal and knows that Marcus would wait for her. She explains that Marcus is a former Baltimore police detective who was shot three times in the heart, and the bullets are still there. Mrs. Frederic prepares to use the medal but Marcus warns that it won’t work against him.
Sykes dons the Bracelet and gets up out of his wheelchair. He then has Pete put the gun to his own head to shoot himself while his mother looks on. However, Myka and Helena manage to reactivate the portal from their end and shoot the crop out of Sykes’ hand. They inadvertently knock the rope from the Marie Celeste
off a shelf and it binds them both together. Artie sprays it with neutralizer fluid while Sykes runs back to the portal.
Jane goes after Sykes and he disarms her. However, she punches him and then runs for the portal.
Marcus prepares to stab Mrs. Frederic, but Claudia arrives and opens the box that Marcus brought with him. It contains Johann Metzel’s Metronome, which Sykes has used to keep Marcus alive. She stops it and tells Marcus that it’s for Steve, and Marcus dies in a matter of seconds.
Jane enters the portal and sykes comes after her. Pete tackles him but Sykes throws him off and enters the portal. As he approaches the other side in Hong Kong, Pete shuts down the portal and Sykes disintegrates as the Collodi Bracelet falls into Jane’s hands. Pete calls to assure his mother that he’s okay. The others arrive and Pete thanks Helena for her help. Claudia calls to tell them that Marcus is dead, but Artie realizes that the emergency lights are still flashing. The barrier is still up and Mrs. Frederic confirms that it should dissipate as soon as the warehouse is no longer in danger.
Artie realizes that Sykes planned to leave his wheelchair behind all along. They open it and find a piece of masonry from the Blitz. It absorbed the concussive force of the entire German Luftwaffe and is rigged to discharge it all. As Artie tries to disable the masonry without success, he explains that the warehouse barrier is designed to contain the blast and protect the world. With two minutes left, Pete tries to use a blowtorch on the masonry.
As Claudia, Leena, and Mrs. Frederic go through the files to find a solution, Claudia looks at the metronome. Mrs. Frederic warns her against using it for personal gain, but Claudia says that she’s tired of the Regents’ arbitrary rules and that she’ll bring back Steve.
Pete is unable to destroy the masonry and they realize that there’s no way out for them. However, Helena reroutes the barrier circuits and creates a smaller field around Pete, Myka, and Artie. Helena smells apples, the same scent she smelled at Warehouse 12, and smile at Myka. The bomb detonates and a fireball sweeps through the warehouse, destroying everything it touches.
At the B&B, the shockwave knocks Mrs. Frederic to the floor. As the warehouse is destroyed, she rots away in a matter of seconds as Claudia and Leena stare in shock.
The barrier finally drops and Pete and Myka survey the destruction. Artie takes out MacPherson’s watch and says that they may not have lost yet.