Claudia is isolated in the Warehouse to face off against Paracelsus, the Caretaker who takes all the care for himself. Claudia knows the Warehouse will protect her, and Artie, Pete, Jinks and Mrs. Frederic believer her - but that doesn't make it any easier to be on the other side of an impenetrable barrier from their comrade. Mrs. Frederic seeks out the Regents while Jinks and Artie try various (painful) methods of breaking through the barrier. It's not until Pete returns from the hospital with Myka (the tumor was benign, the surgery went really well) that she schools them all on reading the freakin' addendums to the manual every now and again. If they had, they'd know that the shield gets its energy from the Alpha Centauri star system, and if they just reposition the contact point, they can walk right through - easy as pie.
It's once they're in there that the trouble starts. Since Claudia is the new Caretaker, she's part of the Warehouse. Thus, Paracelsus isn't able to kill her, but he can control her. He puppeteers her to fetch and arrange several artifacts - a sundial, a pocket watch, and a telescope - which, she believes, make a wormhole-time travel device. When Paracelsus hears Jinks and Pete set their distraction, he sicks Claudia on them, with all manner of deadly weapons. It's not until Artie and Myka re-light the fires in the Eldunari Chamber that the link between Paracelsus and Warehouse 13 is severed, and Claudia is freed.
But by then, it's too late - the big baddie has built his wormhole, and leaps through it just as the crew comes on the scene. Pete tries to go after him, but Artie stops him, throwing a fork into his hand as the Warehouse shudders and becomes an entirely new landscape. No longer their tumbledown, nondescript structure, the Warehouse changes into a gleaming, sterile bunker. The worst part? Paracelsus's face is plastered all over it. Whatever Paracelsus did after jumping through the wormhole changed reality, and it's up to the team to find him, neutralize him, and change it back.
Pete and Claudia file off to find the mainframe of the bunker's computer system, and discover that the hub of all the electronic information is Abigail, transmogrified into a cyborg. It - she - won't tell them the high-level information they seek, but they manage to find a key piece of information - June 10, 1541, the date Paracelsus went back in time - and run it back to Myka, Jinks and Artie, who have assembled all the artifacts necessary for the wormhole machine. They set the device running and Pete and Myka jump through while the others hold down the fort.
The partners find themselves in a field of dead bodies, with a very live agent, Lisa da Vinci, holding a knife to Myka's throat. They finally convince her that the Paracelsus from their timeline is behind the carnage, despite having been bronzed earlier that day in her timeline. From Abigail the Computer, they know that he killed all the Regents on this day, and when the time travelers catch up to him, it's just in time to save the Regents and get after the mad scientist.
In Dystopia-land, Artie turned himself in to divert attention, even though he knows it will mean being a lab rat for Paracelsus's human-artifact experiments. What he didn't realize is that two of his best friends - Vanessa and Hugo - would be the doctors in charge. Although they don't believe in the cause, they must act - Paracelsus has their children. Artie can't convince them to back down, and Artie would be toast if not for Claudia showing up and Tesla-ing them. Actually, he still might be toast - Paracelsus shows up right after her and restrains them both for testing.Back in 16th Century Italy, Pete has tracked Paracelsus back to Warehouse 9, and manages to wrangle the psycho to the floor, where he throws the man's words about wanting to save Myka's life back at him. Just as it's clear the madman won't be winning this round, the antiseptic Warehouse monstrosity turns back to the shack we know and love, and all of our heroes are safe. The forks Artie handed out protected them from shifts in the timeline - not bad thinking, Art!
So Warehouse 13 now has TWO bronze Paracelsus (or a pair o' celsi, as Pete says) and all its inhabitants back, though Claudia's darn icy with Artie for keeping the secret of her sister. And it looks like they have a stowaway: Benedict Valda, the benevolent Regent who died in Egypt in this timeline, was a malevolent general under Paracelsus in the yucky timeline - and thanks to the artifact forks, he managed to sneak through from his reality to ours...