As Myka and Pete arrive at the warehouse they call for Artie and Leena but get no answer. As they enter the office, Pete gets another huge vibe and Myka tries to call Leena. They find her cell phone on the desk and confirm that there are alerts in both the Bronzing Sector and the Dark Vault. The agents split up and Pete confirms that someone has ransacked the Dark Vault searching for someone. Myka tells her partner to come to the Bronzing Sector immediately. When he arrives, he realizes that someone has shot and killed Leena.
The agents check in with Mrs. Frederic and Steve in Rome and she tells them that Artie is under the astrolabe's influence and killed Leena. As Claudia arrives, she realizes that something is wrong and they tell her the news. She insists that it can't be true but Brother Adrian in Rome explains that Robespierre used the astrolabe during the French Revolution and it turned him evil, creating the Reign of Terror. Claudia refuses to believe that her mentor is lost to them and Steve tells her that they're working with Adrian to find a cure. When they wonder where the astrolabe is, Mrs. Frederic explains that she gave it to Helena for safekeeping and then sent her off the grid. As she signs off, Mrs. Frederic warns them that Artie is their most dangerous opponent because he knows all of their strengths and weaknesses.
As Myka and Claudia sign off, Pete sees Leena standing outside on the office catwalk. He goes out but discovers that she has vanished. When Myka and Claudia come out, they admit that they didn't see or hear anything and Peter wonders if he's imagining things.
In Rome, Adrian sits down with Mrs. Frederic and Steve and they go through the Brotherhood library. Robespierre's journal is among the books and they go to work.
At the warehouse office, Artie emerges from the shadows and warns them to stay away from him because he realizes the astrolabe is somehow affecting him. He asks for the artifact so that he can undo the astrolabe's effects but they refuse to give it to him, pointing out that doing so would revert time, destroy Warehouse 13, and leave Steve, Mrs. Frederic and Helena dead. As they talk, an alarm goes off in the IRS Quartum but Artie tells them to ignore it and pay attention to him. Claudia realizes that they're talking to a projected image and Evil Artie warns them that if they don't give him the astrolabe then he will do to them what he did to Leena. They try to get through to him but Evil Artie says that he isn't Artie anymore, and that he will use the astrolabe to set Artie free from 35 years of warehouse slavery.
Claudia realizes that the hologram is being projected on Hugo's internal system, meaning Evil Artie is inside the warehouse. Evil Artie cuts the signal and the alarm continues signaling from the IRS Quartum. A fire breaks out and they go to the sector and put out the fires. Claudia explains that the files from Warehouse 8, during the time of the Holy Roman Empire, were stored in that area. They figure that Evil Artie set the fire to cover his tracks and keep them from learning something vital about his plans.
Steve gets impatient when they don't find anything in the Brotherhood's library. Adrian does find an entry saying that use of the astrolabe will fracture a man's soul, causing him to live as two until the evil from within overcomes the good. Having reached a dead end, Steve and Mrs. Frederic prepare to leave. Steve believe that they can somehow heal Artie but Adrian isn't confident that they can. As they go, he tells them to return to astrolabe back to him... if they find it and can save the world.
As the agents go through the Warehouse 8 records, they realize that the astrolabe as never stored there and that Artie was covering up something else. As Myka and Claudia check on the items awaiting storage, Pete sees the ghostly Leena again. She leads him to a room filled with torture instruments and points to a cabinet before disappearing. Searching, Peter finally finds a secret compartment containing the files on a dagger.
The agents show the files to Mrs. Frederic via the Farnsworth. She explains that Helena gathered the data when Artie had her track down the dagger he dreamed that Claudia would stab him with. Claudia insists that she would never stab her mentor and Mrs. Frederic admits that there's no way to know if the dream is an accurate prophesy or not. They figure that Evil Artie was subconsciously influencing their version, giving him the dream and leading him to the dagger. They discover that the dagger belonged to a Spanish Jesuit living during the time of Warehouse 8. Claudia checks the computers to track Evil Artie using a trick he doesn't know and confirms that he's flying to Budapest under an alias. Claudia tells the agents to go without her so she can't get near Artie and risk making his dream come to true, and Pete and Myka take a flight to Budapest.
In Budapest, the customs officer gets a red flag when he checks Evil Artie's ID and has two security guards take him away.
Pete and Myka arrive in Budapest and confirm that Evil Artie was going to meet with an ambassador who owns the dagger and had loaned it to the Czech Museum in Prague. Claudia informs them that Evil Artie is in custody and that Warehouse 8 contained one of the most dangerous artifacts ever: the Chinese Orchid. The Chinese Emperor used the threat of unleashing Sweating Sickness on the English invaders, driving them back. The disease is fatal within 24 hours and no cure has ever been found. The Orchid is encased in an impenetrable case and they realize that Evil Artie plans to use the dagger to break open the case, unleash the plague, wipe out half the world's population and force them to give him the astrolabe so he can restore the original timeline.
Mrs. Frederick arrives at the Budapest Airport and discovers that Evil Artie has escaped. She checks footage and confirms that he used a ship's barometer to stop time for 47 seconds and get away. Pete and Myka check in via their Farnsworth and inform Mrs. Frederic that they are heading to the Czech Museum... unaware that Evil Artie has tapped their Farnsworth and now knows where to find the dagger.
Steve and Claudia fly to Berlin to visit the insurance company built on the site of Warehouse 8 and recover the Orchid before Evil Artie gets it.
As Pete and Myka search the Czech Museum for the dagger, they both worry that there may be no going back from what has happened. Pete wonders how Artie will cope with the knowledge that he killed Leena if they can cure him, but Myka insists on focusing on the present.
As Steve and Claudia go through the insurance company's sub-basement, Claudia realizes that he's hiding something. He reluctantly admits that they haven't found any way to cure Artie without reversing time. Claudia insists that she'll find a way as they find a hatch leading into a chamber below. Descending, they find a door and Claudia uses a key from the IRS Quartum to open it. Beyond lies an empty cavern, but they find a mark on a wall representing a stone bridge.
Pete and Myka finally locate the dagger in a display case, but Evil Artie steps out. When Pete tries to get through to him, Evil Artie dismisses him as an idiot and a child who wants a father figure. When Myka tells him to stop, he attacks her verbally as well, saying that she hates being the smartest person in the world. When the agents are distracted, Evil Artie tosses a noose up around the rafters. The agents and the tourists all rise into the air, choking, and Evil Artie explains that the noose belonged to famous hanging judge Isaac Parker. He takes the dagger, says that he's done with Artie and Myka, and walks away. Pete manages to swing on the invisible rope, grab a battle axe, and throw it to cut the noose. Once everyone is freed, Myka assures her partner that Evil Artie was preying on their fears and they go after their friend.
In Zittau, Germany, Evil Artie sets up a meeting with Johan Steinbruck at an outdoor café. He shows Johan a cobra basket artifact and Johan realizes that the newcomer is from Warehouse 13.
The agents contacts the others and Claudia shows them the symbol. Mrs. Frederic realizes that stone bridge, in German, is "steinbruck" and explains that Franz Steinbruck was the original caretaker of Warehouse 8.
Franz's descendent Johan calls in his children, Carl and Anya, and Evil Artie explains that knows that the Steinbrucks have watched over the Orchid down through the ages, and that they moved it to keep it safe from the Nazis during World War II. He says that he needs to recover it, but warns that rogue agents are trying to get it and gives the Steinbrucks an artifact to deal with them.
The Steinbruck family takes Evil Artie to the water mill where they hid the Orchid in 1939. The Warehouse 13 agents arrive, guns ready, and Evil Artie tells them that they've already lost. Claudia confronts her mentor trying to get to him, and for a moment she seems to reach the real Artie. Then he plugs his ears and tells Johan to use the artifact finger cymbals. The noise deafens the four Warehouse 13 agents and Evil Artie and the Steinbrucks run into the mill. The agents recover and split up, and Claudia and Steve go up after the Steinbrucks. Claudia uses her Tesla on Johan and then she and Steve tackle Anya and Carl. Carl escapes and runs downstairs.
Pete and Myka follow Evil Artie downward and he tries to use another artifact on them. Myka bats it aside with a board and Pete tackles Evil Artie while his partner runs with the dagger. She finds Steve and helps him knock out Carl, and they find another stone-bridge mark on the wall. When Steve triggers it, he reveals a hidden compartment containing the sealed Orchid.
Evil Artie arrives using Pete as a hostage, and demands that they give him the Orchid in return for the agent's life. When Steve hands it over, Evil Artie tells Myka to give him the dagger. She tosses the dagger beneath the grindstone below and tells Evil Artie that it's over once the stone grinds the artifact to pieces. Evil Artie says that it's over when he says that it's over and then freezes time using the barometer. He then runs down with the Orchid and recovers the dagger from beneath the time-frozen grindstone.
As the 47 seconds elapse, Claudia arrives and tries to get through to the real Artie. Disgusted, he tells her that he's saving Artie from all of them, and dismisses Claudia as a desperate little girl seeking love and recognition. Evil Artie tells her that Artie doesn't love any of them and that they ruined his life.
As the others arrive, Evil Artie speaks the words, "I cast you out" and uses the dagger to shatter the Orchid's container. There's a wave of energy, knocking the dagger out of his hand, and Claudia grabs it. Artie plucks a blossom from the orchid and tosses it into the air, and Claudia realizes that the real Artie wants her to fulfill his dream. She stabs Evil Artie in the chest, saying, "I cast you out," and Pete leaps forward to catch the blossom. He succeeds, but it explodes when it touches his hand. Particles of black energy spread through the air, entering the agents' bodies and then sweeping across Europe and then the world.