Myka and Pete arrive at the warehouse and call for Artie and Leena. Pete gets an even worse vibe and Myka calls Leena. They hear her cell phone on the desk and Myka confirms that there are alerts in the Dark Vault and the Bronzing Sector.
Pete goes to the Dark Vault and discovers that someone has torn through the place. He calls Myka and she tells him to get to the Bronzing Sector immediately. She tells him that they're not okay and to hurry. When Pete arrives, he realizes that Leena' has been killed with a gunshot.
The agents call Mrs. Frederic in Rome, and she tells them that Artie killed Leena and what he has gone through. Claudia arrives at the warehouse from Menlo Park and realizes that something is wrong. She insists that it can't be true but Mrs. Frederic admits that an evil has been created: Artie. Adrian explains that Robespierre used the astrolabe during the French Revolution, leading to the Reign of Terror. Claudia refuses to give up on Artie and Steve assures her that they're trying to find a cure. Mrs. Frederic explains that she entrusted the astrolabe to Helena and even she doesn't know where it is. She also warns the agents that Artie knows all of their strengths and weaknesses.
As Myka cuts off the Farnsworth, Pete hears Leena's voice and looks outside and sees her on the balcony. He runs out but no one is there and the others didn't see him. He realizes that Leena couldn't have been there and that he must have imagined things.
In Rome, Brother Adrian reviews the history of the astrolabe and assures Steve and Mrs. Frederic that they will find what they need in the Brotherhood's library. He explains that they are under the protection of the Vatican and value knowledge, and shows them Robespierre's journal. There isn't much but Mrs. Frederic says that they have to begin somewhere.
At the warehouse, Artie suddenly returns to the office. Claudia runs to him but Artie tells her to stay away because there's something wrong with himself. He refuses to remember what he's done but knows that the astrolabe is affecting him somehow. Artie tells them that he has to reverse astrolabe's effects and undo what has been done to him, but they refuse to let him use it. They remind him that he said that using it would destroy the warehouse and kill Steve, Helena, and Mrs. Frederic. The IRS Quartum suddenly sounds an alarm but Artie says to ignore it. When Claudia reaches for him, she realizes that he's using Helena's hologram device and demands the astrolabe from them. He warns them that telling them where it is a safer choice and reminds them of what he did to Leena. Artie insists that he is not Artie anymore and that he will use the astrolabe and set Artie free from 35 years of slavery to the warehouse.
The hologram images flickers and Claudia realizes that Artie is using one of Hugo's projection devices from inside the warehouse. Artie vanishes and the alarms go off from the IRS Quartum. An incendiary device explodes, setting a section of the warehouse on fire. They run to the section and Claudia seals the doors while the agents put out the fire with extinguishers. The files from Warehouse 8 from the Holy Roman Empire age were stored there and they figure Artie destroyed the crates to keep them from learning something about the astrolabe.
Steve and Mrs. Frederic find nothing and Steve soon grows impatient. Adrian finds an entry about how a man living the same day will fracture and live as two until only one remains. According to the book, evil will overcome goodness and the evil will come from within. Steve suggests that fractures can be healed and there must be a way to reach Artie's good side. Adrian tells them that they should leave and wants his astrolabe back if everything works out.
The agents go through the records on Warehouse 8 and confirm that the astrolabe was never there. They realize that Artie has a plan but they're missing something. Some of the inventory wasn't entered into the computer so Myka and Claudia go to check the manifest. Pete sees Leena again before she fades into a wall and he follows her into a room filled with instruments of torture. Leena points to a cabinet and Pete finds nothing inside. When he turns to Leena, he discovers that she has disappeared again. Turning back to the cabinet, Pete works out that there is a secret compartment containing files on a dagger
The team shows the files to Mrs. Frederic, who explains that the files are the research Helena gathered on the dagger. Artie asked her to find the dagger because he was having a vision of Claudia stabbing him with it. Claudia says that she never would have done it and Mrs. Frederic admits that it may not come true. When Pete mentions that Leena led him to the dagger, Mrs. Frederic takes an interest and Myka suggests that the dream was Artie's dark side's way of leading his good side into finding the dagger. They confirm that the dagger belonged to Spanish Jesuit during the Holy Roman Empire and Claudia goes to find a way to track Artie cybernetically. She realizes that he would have anticipated her but Claudia uses a new trick that Artie doesn't know. They confirm that he's heading to Budapest to see a man about a dagger and Claudia agrees to stay there so she can't fulfill the dream, while Pete and Myka head for Budapest.
In Budapest, Artie arrives at the terminal and the security desk gets a red flag on his passport. Security guards lead him away.
When Pete and Myka arrive, they confirm that Artie was going to meet with an ambassador who loaned his art collection to the museum in Prague, including the dagger. Claudia tells them that Artie is being held as a terrorist and informs the agents that the deadliest artifact in Warehouse 8 was the Chinese Orchid. It releases a disease called English Sweating Sickness and the Chinese emperor used it to force the English to back off. No cure was ever found and the Orchid disappeared. It's encased in an impenetrable case and they figure that Artie will use the dagger to open the container, obtain the orchid, and unleash the disease. When the disease wipes out half the world's population, the agents will have no choice but to give Artie the astrolabe to reverse time again.
Mrs. Frederic arrives at the airport and discovers that Artie has subdued and tied up the two guards after using an artifact. She reviews the security footage and confirms that Artie used a barometer to stop time. She tells the agents, who confirm that they're heading to the Prague Museum. They're unaware that Artie has tapped into the Farnsworths and learns where he has to go.
Steve and Claudia fly to Berlin to look for the Chinese Orchid. Claudia says that they're going to Warehouse 8's previous location to get the Orchid so that Artie won't. They go to the insurance company build over the site and left the Orchid buried deep below.
At the Czech Museum, Pete and Myka are both worried about losing one of their own. Pete says that he doesn't know how they can tell Artie that they killed Leena but Myka says that they need to focus on getting through the present as they go to the gallery with the dagger.
As they go through the tunnels, Steve tells Claudia that Adrian is still digging for information about the astrolabe. Claudia realizes that he's hiding something and demands the truth. He finally says that everything they've found indicates that they can't heal Artie without reversing time via the astrolabe. Claudia vows to find a way to bring Artie back and they find a hatch leading downward to a locked door. She uses a key from the IRS Quartum to open the door but there's nothing there but an empty cave. There is a mark on the wall representing a bridge with a river running through its mouth.
Pete and Myka look for the dagger and find it among a collection of other knives. Myka spots Artie nearby and tries to get through to him. He demands the astrolabe and dismisses Pete as an idiot who desperately wants Artie as a father figure. Artie dismisses Myka as a rigid prude and while the agents stare, momentarily taken off-guard, Artie takes out hanging judge Isaac Parker's noose, loops it around the rafters, and uses it to suspend everyone in the room by invisible ropes. He then takes the dagger, says that he's done with the agents, and leaves.
Once Artie leaves, Pete swings over to a battle axe mounted on the wall and throws it, cutting the noose loose. Everyone falls to the floor and the agents wonder if that's what Artie really thinks about him. Myka says that Artie knows what they fear and used it against them, and they set off to get the dagger back.
In Zittau, Germany, Artie goes to a café, puts a straw basket on a table, and a snake emerges from it and threatens the man seated at the table, Johan Steinbruck. Artie then closes the lid, sealing the snake away, and the man realizes that Artie is from the warehouse.
The agents update Mrs. Frederic and Claudia and Steve show her the drawing on the wall. Mrs. Frederic tells them that the German word for "bridge" is "brucke," and the symbol indicates Franz Steinbruck, the caretaker of Warehouse 8.
Johan's children, Carl and Anya Steinbruck, arrive at the café and Artie explains that he showed them the basket to confirm that he is from Warehouse 13. They have guarded the Orchid since World War II and Artie claims that rogue agents are after him to get the Orchid. He wants the Steinbrucks to show him where the Orchid is and gives them weapons to deal with the agents following him.
The Steinbrucks take Artie to a water mill and explain that the Orchid has been there since 1939. Pete, Myka, Claudia, and Steve arrive but Artie tells them that they've already lost. Claudia tries to get through to Artie, asking him to trust him. Artie plugs his ears and tells Johan to use the finger cymbals that he gave him earlier. The agents are deafened while the Steinbrucks and Artie go into the water mill. The team splits up and Claudia and Steve follow the Steinbrucks upstairs. Claudia stuns Johan and then she and Steve fight Anya and Carl. Carl escapes and Steve goes after him while Claudia wrestles with Anya.
Pete and Myka follow Artie downward and spot a trapdoor in the floor. As Pete opens it, Artie throws a web-artifact at them and Myka bats it aside. Pete tackles Artie while Myka runs off with the dagger and helps Steve knock out Carl. Steve finds the symbol on the wall and presses the brick, revealing a hidden compartment. Inside is the Orchid within the container.
Artie arrives, holding a gun to Pete's head, and promises to shoot him if they don't give him the Orchid. Steve brings it over and Artie tells Myka to give him the dagger as well. Pete tells her to do it but Myka throws it down into the mill and Artie prepares to shoot. Myka tells Artie that it's all over and asks him to let Pete go because the dagger will be ground to pieces. Artie aims the gun between the three of them, says it's over when he says it's over, and then uses the barometer to freeze time, take the orchid, and goes down to get the dagger from beneath the frozen grindstone.
Claudia runs in and tells Artie that he's still in there and it's not too late. He looks at her briefly but then says that he's saving Artie from all of them, particularly Claudia who is a desperate girl child. Artie tells Claudia that Artie doesn't love any of them and that they ruined his life. As the others come down, Artie shatters the Orchid's case with the dagger. The burst of energy throws it into the rafters and Claudia grabs it. Artie tosses the orchid flower into the air and she realizes that she wants him to do it. Claudia stabs him in the chest as the orchid falls to the ground. Pete catches it but it disintegrates into a wave of black energy that spreads out, infecting all of them, and then going out into the world and spreading across Europe.