Nick tells Paracelsus, his uncle, that the unconscious Claudia is no threat. He gives him a pair of glasses that downloads information on everything that occurred since Paracelsus was bronzed, bringing his uncle up to speed. Paracelsus thanks Nick for freeing him, and Nick asks him to lift the curse of immortality from himself and his mother.
Later, Pete and Myka review the recording of the incident using the durational spectrometer and try to determine why there's nothing in the system on why Paracelsus was bronzed. They can't read lips, and Myka discovers that several artifacts are missing. The agents check the durational spectrometer again and see Paracelsus slap Nick. Meanwhile, Artie and Steven put Claudia back in the bronzing unit and prepare to free her after Artie repairs the damaged unit. However, it doesn't work and Artie discovers that a bronze stele artifact that make the bronzer works has been taken. A chemical message ignites, triggered by the light when Artie opened the panel. It says "Sutton knows what I want" and they figure that it's a ransom note.
At the B&B, Abigail stands guard over Charlotte, restrained with the Folsom Ball & Chain artifact. Artie and the others arrive and demand to know where Nick and Paracelsus are. Charlotte insists that they were supposed to wait for her, and that Nick liked Claudia. Myka figures that Paracelsus slapped Nick when the teenager refused to go along with his own plans, and Charlotte realizes that the alchemist has betrayed her as well. She explains that Paracelsus is Sutton's brother, and as an alchemist he combined science with multiple artifacts.
In the 16th century, Paracelsus pays Sutton to participate in his immortality experiment. However, the alchemist drugs his brother's wine and reveals that he has Charlotte and Nick as well, and plans to perform his experiment on all three of them. Paracelsus then used the Philosopher's Stone combined with an Egyptian copper bowl to create fumes that made them immortal.
Charlotte explains that Paracelsus was abducted by agents from Warehouse 9 and bronzed. She was forced to watch as Nick fell in love with women, starting with a young girl named Sophia. She grew older and eventually forgot Nick, but he never forgot her. It took centuries until Nick realized that he was cursed to loneliness. However, she needs Paracelsus to reverse the immortality using the same mixture of artifacts. Charlotte thought he would be grateful for his freedom and would cooperate, but now they realize he'll try to give himself immortality. She tells the agents that Paracelsus will head for his laboratory in what was Constantinople, but she only knows it was somewhere beneath the city. Artie figures that Sutton will know where to find the lab and sets out to find him.
Eleven hours later, Artie is still searching the Internet for Sutton's trail. Myka and Pete stay out of his way and Pete asks why she hasn't started her cancer treatments. She insists that it's a personal matter and she'll handle it, but Pete points out that people can't "handle" cancer. Before he can pursue the matter, Artie yells that he has found Sutton. He explains that Sutton is posing as a Russian businessman, Vladimir Kamenev, and is currently in Luxembourg dating a rich duchess. The duchess is throwing a dinner party and Artie tells the agents to head there and take Charlotte with them.
As they go, Artie receives a message tube. Before he can read the message, Steven calls him to the bronze sector. Claudia's Farnsworth is dissolving and Artie realizes that Paracelsus used the stele to bronze her outside of the bronzer. He condition is unstable and eventually she will crumble to dust. Artie and Steven return to the office and check the files for everything they can on bronze artifacts. The computer slows down just as Mrs. Frederic arrives. She appears confused and says that there's something off in the warehouse. They tell her what happened to Claudia and she says that she has to access the restricted files, and then walks away. They realize that something is seriously wrong because Mrs. Frederic never walks away.
Pete, Myka, and Charlotte arrive at the dinner party and spot Sutton. The duchess welcomes her guests and explains that she and Sutton are engaged to be married. Charlotte explains that Sutton is running a con so that the duchess will bring out her gems so he can steal them. Sutton leaves suddenly when he spots them and the agents go after him.
Mrs. Frederic leads Artie to a storage room and has him open the door. She then uses a device to trigger the door, revealing the real storage room, and goes inside to check the files while Artie waits outside. However, she discovers that the file she wants is redacted. Meanwhile, Steven comes in and warns Artie that Claudia's condition is worsening. Artie directs him to a stabilizing device while checking a file, and tells Steven that he'll explain later.
Sutton takes the duchess to a private room for a tryst, but secretly drugs her champagne. Once they share a toast, she collapses out and Sutton relieves her of her gems. However, Pete and Myka burst in and put Sutton arrest. The duchess calls for her guards but Charlotte comes in, says that she's Sutton's wife, and shoots him dead.
At the warehouse, Mrs. Frederic emerges from the storage room and tells Artie that the Regents at Warehouse 9 redacted the file on Paracelsus. She starts to contact Kosan but then sits down, confused. Artie gets her attention and Mrs. Frederic repeats what she just said, and then walks off.
The duchess runs to Sutton, who comes back to life. While she faints at the sight, the duchess' guards run in and Pete, Myka, and Charlotte take them out. Sutton escapes in the confusion, and the agents have Charlotte stay there while they search for Sutton.
Steven hooks up the device to monitor Claudia's vital and admits that he misses her constant chatter. He assures her that they'll save her and remembers all of the times that she's saved them. Steven realizes that he's not getting a signal on her vitals, just as Artie calls and says that he can boost her genetic material on a cellular level to hold off the disintegration. He needs a blood sample from a family member but can't reach her brother Joshua. Desperate, Artie leaves a voice mail and hopes that Joshua will get back to him rather than force him to take the next step.
Pete and Myka chase Sutton through the duchess' manor. He sets more security guards on them but they fight past them and Pete manages to grab Sutton before he can escape.
Kosan arrives at Artie's office and tells him that he's met with Mrs. Frederic and it doesn't look good. The Regent says that there is something more urgent they need to check and goes into the storage room. Contained within it is the Eldunari, the warehouse's central nervous system. It links the caretaker's mind to the soul of the warehouse. The symbols are moving in harmony at first but start slamming into each other and tearing apart. Kosan explains that Mrs. Frederic's mind is a mirror of the Eldunari, and both of them are deteriorating.
The agents take Sutton back up to the duchess' bedchambers and she slaps him, furious. Once she leaves with her security guards, the agents explain that they need his help. Myka explains about Paracelsus and Sutton notes that he developed the bronzing process. When he realizes that Charlotte freed Paracelsus, he blames her for the entire mess. Sutton figures that Paracelsus is insane rather than just eccentric, and remembers what happened when they realized the full extent of his brother's "gift."
When he realizes that he and his family are immortal, Sutton confronts Paracelsus, who boasts of his triumph. The alchemist stabs Sutton in the chest, demonstrating that he can't die, and explains that he killed each of them a dozen times when they slept. However, Paracelsus tells Sutton that he had to kill an entire village for what he needed to make them immortal.
Sutton went to the authorities and had his brother arrested rather than let him kill more people. However, the agents of Warehouse 9 got word and captured Paracelsus, bronzing him. Rather than turn the Philosopher's Stone over to the Regents, he split it in half and hid the two parts. Sutton used the crystal inside the Stone to make a ring that allowed him to restore plants so that he could entertain for money. Paracelsus took the ring from the warehouse, but Sutton has the other half of the Stone safely locked away. He insists that he wants his son back before Paracelsus can complete the plan he had in mind before his capture. Sutton knows that Paracelsus' lab is beneath the Monastery of Stoudios in Istanbul.
Steven uses a radio artifact to contact Claudia. Before he can explain what's going on, Artie calls to tell Steven that he knows where Joshua is, but he has to go there in person. Steven tells Claudia that Joshua's DNA can stop the deterioration, but lies and tells her that her condition is fine for the moment.
The agents, Charlotte, and Sutton go to the Monastery. Sutton explains that he bribed the locals to keep the lab intact, and has been trying to find a way to restore Nick's mortality. They split up, Myka with Sutton and Charlotte with Pete. Nick cries out and Charlotte runs to her son before Pete can stop her. Pete finds Myka, who explains that Sutton ran off. They enter a central chamber and spot the bronzing stele on the wall. There's a pattern of life-related symbols on the walls. Before Myka can work out the pattern, they set off a trap and fall through to a chamber below. They're knocked out by the impact and Paracelsus merges from the shadows to take one half of the Stone from Pete.
At the warehouse, Steven puts Claudia back in the bronzer along with a binnacle that sucks out oxygen, slowing down the deterioration, but it doesn't work. Artie arrives with an atomized blood sample and injects it into Claudia. The disintegration slows and Artie warns that he has only delayed things for 14 hours.
Myka and Pete wake up and they realize Paracelsus has one half, and then start climbing to the trapdoor above.
Charlotte and Sutton find each other and then find Nick in Paracelsus' lab. The alchemist steps forward and immobilized Sutton with an artifact fishing net, and then takes the other half of the Stone. Paracelsus takes out the ring's crystal and puts in the reassembled Stone, and then places it with the Egyptian bowl. Finally he extends the fuming Stone forward and invites them to breathe so they can regain their mortality. They do so and Paracelsus tells Sutton that he will have his revenge for Sutton turning him over to the authorities. The alchemist draws a gun and shoots Nick, but Charlotte throws herself in the way, taking the bullet meant for her son.
Pete and Myka arrive and Pete fires his Tesla, but Paracelsus deflects it with an artifact rod and then throws the rod at the supports, bringing the monastery down. He grabs the Stone and the bowl and runs out, and Pete goes after him. Myka tells Nick and Sutton to get Charlotte out while she goes to get the stele. A support comes down on Charlotte and Pete comes back to try and help. Sutton apologizes to his wife and she tells him to get out before it's too late. Charlotte tells him to look after their son and tells Nick to live his life now that he has one. Myka returns with the stele as Charlotte dies, and the agents get Nick and Sutton out.
At the warehouse, Kosan tells Mrs. Frederic that the Regents have agreed to uncover the expunged files concerning Paracelsus. The Keeper, who maintains the files in their living memory, is the failsafe. Abigail comes in and apologizes to Mrs. Frederic for keeping her identity a secret. The psychotherapist uses a Hawaiian palaoa that holds the memories of past warehouses. Abigail releases them and explains that Paracelsus posed a threat to all of mankind so the Regents bronzed him.
The agents get the stele to Artie, who uses it to free Claudia. Realizing how close they came to losing Claudia, Pete tells Myka that none of them have as much time as they think. He insists that she get it taken care of so that he won't regret all the years he wouldn't have to spend with her. Myka agrees to book an appointment and asks him not to hug her because she'd start crying. Meanwhile, Claudia realizes that she's feeling the Eldunari. Mrs. Frederic and Kosan arrive, and Mrs. Frederic explains that she's losing the battle for control of the warehouse. However, she's not vying for control with Claudia: she's struggling against Paracelsus, who was the caretaker of Warehouse 9. The strain becomes too much and she collapses.