With hundreds - and soon millions - of people around the world suffering from the Sweating Sickness, and Artie alive but unconscious after being stabbed with an artifact by Claudia, the Warehouse team find themselves in a greater crisis than ever. Jane Lattimer has an artifact that allows someone to access another person's subconscious, and she takes Claudia and Jinx to perform that task and save Artie. Mrs. Frederick, Pete, and Myka, meanwhile, try to solve the problem of saving the world from dying of a medieval disease.
They reason that, since the blue orchid was the cause of both epidemics, it must have been reconstituted somehow in order to strike twice. They hunt the archives for artifacts that bring flowers back to life, and though they don't find one at first, they do learn of a man in Marie Antoinette's court, the Count of Saint Germain, who was able to do this. Pete and Myka travel to Columbia University to meet with the foremost scholar on the count, but when they arrive, he's completely drunk.
Myka's threats of violence - and the promise of an adventure with government agents - rouse Professor Sutton enough for him to be able to tell them that the count always wore an impressive ring, but that ring is buried with the count in the catacombs under Paris. In order to navigate the underground tombs, Pete and Myka need Sutton's help - he not only has the map, but knows where to find the legend of the map: the house of his rival, Charlotte Dupree, in Paris.
The three of them go overseas while Claudia and Jinx search the catacombs of Artie's mind, disguised as the Warehouse. It's guarded by figments of Artie's imagination in the forms of Vanessa, Mrs. Frederick, and finally, MacPherson, to whom Jinx sacrifices his presence in Artie's mind so that Claudia can make her way unhindered to where Artie is - his office. But when she arrives, he orders her to leave, saying she'll ruin everything, and when the figure of Leena walks in, Claudia realizes that Artie is hiding in a good memory in order to avoid a bad reality.
Claudia reminds him that in Germany he begged her to save him from some evil inside him that made him kill Leena, and Leena's death was not Artie's fault. When Claudia plunged the artifact into his heart, she knew it would purge the evil that formed when Artie used the astrolabe, and now she tells him she won't ever give up on him. The argument becomes so violent that she pushes him out of the door, and both of them find themselves awake and in their bodies, unharmed but badly shaken.
Pete and Myka are frustrated with their "partner", but he bites back by saying he's heard the rumors that this new sweating sickness is caused by a rare orchid, and he knows that's why their after the ring. They break into the house and look for the legend, but Charlotte surprises them with a shotgun. Myka sees a portrait that prompts her to zap Charlotte with the Tesla, then turns the portrait to face Pete: it's Sutton when he was at the court of Marie Antoinette, going by the name Saint Germain. Sutton quickly explains that he is there to help - in fact, he found the legend - but the wish to retake some of his possessions, nicked by Charlotte, was too great.
Once inside Saint Germain's tomb, Myka moves toward the ring while Sutton steals a famous diamond placed on the casket by Marie Antoinette, setting a range of poisoned darts flying. Sutton throws himself in front of one that rockets toward Myka, sacrificing himself for the cause. They place the artifact on what's left of the orchid, and all around the world, the sickness leaves peoples' bodies. They carry Sutton out of the tomb, the diamond still in his pocket. Later, Charlotte arrives looking for this same gem, and seeing the pool of blood on the ground, knows that Sutton is dead, but her search for the diamond is begun.
At the Warehouse, Artie mourns Leena and Mrs. Frederick tries to help him forgive himself, but when she turns away, her face reveals her deeper worry for Artie's mind.