The team is working in overdrive to find Paracelsus before he kills again, but when someone shows up in San Francisco hospitals curing terminally ill patients, they find an unlikely suspect. The man, who carries a bowl emitting a glowing, gold light, matches the description of Paracelsus. But why did he go all the way from Istanbul to California, why is he healing people, and why is he muttering strange phrases about air yielding stone?
Nick, who's furious at his father for oh so many things, has an outrageous fight with his father, the sulks away to the office, where Claudia is trying to figure out why the heck Paracelsus is acting so weird. The key may be in Nick's description of the lab where he was immortalized, which was covered with a cold material feeling like stone but looking like wood. This - petrified wood - must be critical to his process, and the easiest place to access massive amounts of the stuff is now Coit Tower in San Francisco, which, unbeknownst to those not in the Warehouse, has a false wall built of petrified wood.
Since Paracelsus is connected to the Warehouse as its erstwhile Caretaker, he must be brought back alive in order to save Mrs. Frederic. Artie comes up with a genius idea to use the ribbon that disconnects Caretakers, wrap it around a projection artifact, shoot it with a Tesla through a Farnsworth and disconnect Paracelsus remotely. Unfortunately, Sutton - stinging from the bout with his son - shows up and ruins the whole thing while trying to play hero and make up for this whole mess to his son. His clumsiness alerts the scientist to the plan, who gains immortality after blasting everyone with their own Tesla beams and dashing, leaving Pete to give chase. Pete finally traps him with the help of Claudia's city-hacking abilities, and brings him back to the Warehouse to be bronzed.
We said, "back to the Warehouse to be bronzed." Ahem. Why isn't he bronzing? Oh right, because he developed the bronzing process and knows how to alter his body chemistry to prevent it. It's a good thing Nick and Sutton made their peace and headed off to live their now-mortal lives with new name. As Mrs. Frederic gets worse and worse, Pete and Artie decide to throw Paracelsus in a suspension artifact made of blue light, and Pete does his best to get the answers for how to save Mrs. F. Paracelsus informs Pete that Mrs. Frederic isn't the one he should be worried about; it's Myka. She's dying, even now as she lies unconscious under her doctor's care and undergoes surgery to fight her cancer. The cancer has spread, or so Paracelsus tells Pete - he can see it in her eyes.
Pete knows that Paracelsus can save Myka, so he makes a deal: he'll wipe Paracelsus' mind clean so he doesn't have to endure his own thoughts for all of eternity in the bronzer, and Paracelsus will cook up something special for Myka. But to make sure he can keep Paracelsus in line, Pete first makes him immortal. But the madman doesn't tell Pete that use of the philosopher's stone in close proximity to the Warehouse makes his connection exponentially stronger, and he now has complete control of the Warehouse. He can use the artifacts with telekinesis, and Claudia feels this shift and disconnects Mrs. Frederic from her duties. That means she's safe - for now - but stewardship moves from Mrs. Frederic to Claudia.
They realize they must flee, but Claudia won't go - she's at a crossroads. Artie has just told her his apocalyptic confession that he didn't get the DNA sample that saved her from Joshua - he got it from her sister, Claire. He's known her sister was alive, and not killed in the car crash that killed Claudia's parents, since before he met Claudia. He tried to protect her from the truth, since her sister is a very dangerous woman, but Claudia knows she has to take care of herself. And, she knows that the Warehouse will take care of her as she faces off with Paracelsus. Mrs. Frederic sees the truth in her protégée and orders everyone else out. They will fight Paracelsus from the outside - and Claudia from within.