Episode 1: Endless Terror
Last episode (which was also the final episode of Season 4), Paracelsus tapped into the Warehouse and took control. Artie, Steve, Mrs. Frederick, and Pete left right before Paracelsus erected a force field around the Warehouse, but Claudia stayed behind. She figured since she’s slated to be the next Caretaker, she already has a bond with the place and it’ll protect her from Paracelsus. This episode starts with Claudia confronting Paracelsus and her theory
seems to hold up; the Warehouse may be under Paracelsus’s control, but it won’t kill Claudia because she’s already part of it. Unfortunately, that means Paracelsus can control Claudia and he quickly forces her into the office where he uses Orville Wright’s Goggles to read Claudia’s mind. He learns of H.G. Wells’s Time Machine (among other things) and forces Claudia to help him find artifacts so he can construct something, though he doesn’t tell her what it is.
Pete picks up Myka from the hospital; her cyst turned out to be benign and 
she says everything’s fine, so I guess she doesn’t have cancer after all. Pete fills her in on what’s been happening. Outside the Warehouse, Artie covers a rented car in purple neutralizer goo and tells Steve to drive really fast straight at the force field. Mrs. Frederick calls to tell them the Regents are on some kind of retreat in Europe, so they’re pretty much on their own. Steve slams the car into the force field, but nothing happens (well, the front bumper gets smashed in). Artie has another idea … one that involves a crowbar and a parking lot full of cars.
Pete tells Myka everything that happened and she wonders how Paracelsus got control of the Warehouse in the first place. Pete admits he brought Paracelsus the artifacts that helped him get free and take over, but Pete can’t bring himself to say why he handed those artifacts over … because
Paracelsus promised to use them to save Myka from her cancer. Myka remembers something about the force field and tells Pete to get them to Innes Observatory as fast as possible. Back outside the Warehouse, Artie’s big plan involves a bunch of car batteries he apparently stole. (Artie: “Oh please, of all the illegal things I’ve done, this is probably the least illegal”.) When they try to blow open the force field with the batteries, Steve gets thrown about fifty feet.
Pete and Myka show up and Myka explains that she read something in one of the addenda to the Warehouse Manual (which even Artie hasn’t gotten 
around to); the Regents built a fail-safe into the Warehouse force field, which draws its power from Alpha Centauri. Once the fail-safe (located at Innes Observatory) is turned on, the force field will look solid, but Warehouse agents can walk right through, as Myka demonstrates. Steve is pissed off that they could’ve just walked in all along, but he follows the others inside. Artie says he thinks he can realign the Eldunari (the heart of the Warehouse), taking control away from Paracelsus. He takes Myka with him, leaving Pete and Steve to create a diversion.
Pete creates the diversion by knocking random shit off the shelves. That does get Paracelsus’s attention, but he sends Claudia—still under his control—to take care of things. She uses a bazooka, Tommy guns, and a bunker bomb to try and kill Pete and Steve. Luckily she misses each time,
but not by much. Artie and Myka use Sargon’s Mirrors to redirect the flames of the Eldunari back into their proper alcoves. It takes a minute for all the alcoves to light up, but when they do, Paracelsus’s control of the Warehouse—and Claudia—is broken. Just in time too, as Claudia is about to skewer Pete and Steve with a crossbow bolt. Paracelsus is pissed off, but he’s pretty much finished his next project, so he figures it doesn’t matter.
Claudia fills the others in on what Paracelsus has built … a time machine. While H.G. Wells’s Time Machine only sends someone’s consciousness back in time, Paracelsus is cobbling together a number of artifacts that will allow him to time travel physically. Pete remembers how Paracelsus had him 
gather a couple of artifacts and he almost blurts out that he helped Paracelsus in order to save Myka. Artie has some ideas on how to take care of Paracelsus, starting with the arrow that killed Achilles. But Paracelsus has already activated his time machine and is preparing to step through when the others show up. Pete fires Achilles’ arrow, but it misses and goes through the time portal … followed seconds later by Paracelsus. Artie hands everyone a small fork just as the Warehouse changes around them. The Warehouse goes from the crowded-and-grungy Steampunk place we all know to an austere space that looks like it was designed by George Orwell. They soon realize that Paracelsus did something in the past that changed everything … and that Paracelsus was the Caretaker of Warehouses 9 through 13.
Artie figures history can’t have changed too much (other than for the Warehouses) since a quick look around seems to show that history unfolded the way they remember. Artie explains that the forks are from Versailles (which used to experience time-slips) and kept them from being affected by
whatever changes Paracelsus did make in the past. (Pete: “Luke, use the forks!”) Claudia checks out the computer interface and it’s really advanced; apparently Paracelsus has dedicated the Warehouse to scientific advancement above everything else. A hologram of Paracelsus appears, asking if they want help. (Steve: “He’s like that annoying paper clip.”) Claudia says the computer won’t be easy to hack …it seems almost organic, like it can think for itself.
Claudia takes charge (silencing Artie’s objections by reminding him how he lied about her supposedly dead sister), taking Pete with her to find the computer’s hub and leaving the others to reconstruct the time machine. 
Pete tries to get Claudia to spill about what’s up between her and Artie, but they’re interrupted by a quartet of soldiers who’ve been enhanced with artifacts. Pete and Claudia realize Paracelsus must be replicating artifacts and using them to create super-soldiers. They’re in for another shock, as the soldiers’ commander turns out to be Benedict Valda, who’s giving them telepathic commands. The mainstream Valda died a hero in Egypt, but this one is obviously a bad guy … and he seems to sense them watching him, though he doesn’t do anything about it.
While gathering artifacts to rebuild the time machine, Artie, Myka, and Steve run across people being experimented on with various combinations of artifacts. Artie is reminded of the Nazi’s experiments in the camps during
World War Two and says they need to stop this shit fast. Pete and Claudia find the computer hub … it turns out to be Abigail, Keeper of the Warehouse’s knowledge in mainstream history. Paracelsus has managed to harness her brain to power the computers, but without knowing how she’s attached, they don’t dare unhook her for fear of killing her. Claudia tries to get info about how history has changed.
Artie and the others have rebuilt the time machine, but he thinks they’ll need an alternate power source to bring Pete and Myka back from the past. 
Alarms start going off just as Pete and Claudia show up with the info they need … Paracelsus changed history on June 10, 1541, the date when all the Regents of Warehouse 9 were mysteriously killed. After that, no new Regents were ever appointed, so Paracelsus has been running things unchecked ever since. Pete and Myka head through the portal and Artie leads the super-soldier guards on a wild goose chase, telling Claudia and Steve to keep the portal open so Pete and Myka can get back.
In 1541, Pete finds a bunch of dead bodies, including one with Achilles’ arrow sticking out of it. He figures he’s going to get blamed for that, but he has more a immediate problem … a woman is holding a knife to Myka’s throat. She turns out to be Lisa DaVinci of Warehouse 9 (Leonardo’s granddaughter) and she thinks Pete and Myka killed her fellow agents. (Lisa is played by Rebecca Mader from Lost and Once Upon a Time.) Pete explains
—in his best Shatner voice—that they’re time travelers from the future, but Lisa’s not impressed, since her grandfather has been working on time travel for years. Myka disarms her and says Paracelsus is the one who killed all theses people. Lisa thinks that’s impossible, since Paracelsus was Bronzed that very day. Back in the Warehouse, Artie tries to get through to Valda, but he doesn’t believe in multiple timelines. Of course, Paracelsus knows why Artie is there and brings in a couple of doctors to get answers from Artie about his associates and what they’re planning. The doctors turn out to be Hugo (Artie’s old friend) and Vanessa (Artie’s sometime girlfriend), though neither of them recognizes Artie.
Steve is now pedaling a stationary bike to keep the portal open, while Claudia goes to find Artie. Artie tries to get through to Hugo and Vanessa 
and soon figures out they’re scared shitless to say anything negative about Paracelsus. Not only are they being constantly monitored, but Paracelsus holds their children hostage. (Yeah, in this reality, Hugo and Vanessa are married.) Artie finally gets through to them by telling them stuff nobody else knows about them. In 1541, Lisa uses a low-tech version of a durational spectrometer to show what happened in the corridor: Paracelsus came through, found Achilles’ arrow stuck in a beam, and slaughtered the guards who came to grab him.
Pete hits on Lisa (naturally), but Myka reminds them the Regents are in danger. Lisa says the Regents meet in a secret place and Pete talks about how in the 21st Century they meet in public places … coffee shops, TGIFriday’s, Olive Garden. Lisa figures that’s where they are, the olive
garden. (Pete: “Seriously? White chocolate raspberry cheesecake—do not tease me!”) In the Warehouse, Paracelsus senses Claudia’s presence and goes to check which artifacts have been moved. Artie tries to reason with Hugo and Vanessa, but they’re too scared to help him. Claudia shows up and Teslas them, then tells Artie he has to stop trying to shield her from everything. Before Artie can answer, Paracelsus and Valda show up with a security guard.
In 1541, Paracelsus interrupts the Regents’ meeting (which is taking place in an actual olive garden) and demands to be made Caretaker with no 
interference from them. They refuse and he uses an elephant tusk that manifests pythons from the ground. The snakes start squeezing the Regents to death. Pete and Myka are ready to go after Paracelsus, but Lisa summons a huge purple bird to grab the tusk and fly away with it. Lisa explains that the purple bird is used to neutralize artifacts; hmmm, purple bird in 1541, purple goo in the present … I wonder if the goo is made from the bird’s blood? Or maybe it’s the bird’s crap? Anyway, they chase Paracelsus, who runs back to Warehouse 9 to try and take over the Eldunari again.
In the Warehouse, Hugo and Vanessa are preparing to use Alice Liddell’s mirror on Artie and Claudia, who ask if Hugo will take a photo before he starts experimenting on them. Obviously, they’re trying to get Hugo trapped in the mirror. The computer detects Steve near the time portal and
Paracelsus and Valda head over to get him. In 1541, Pete tracks down Paracelsus and throws the scalpel (which is one of the artifacts Paracelsus claimed could save Myka and which Pete’s been carrying ever since) into Paracelsus’s leg, then jumps him. In the Warehouse, the “other” Paracelsus feels the pain in his leg too. In 1541, Pete gives Paracelsus shit for manipulating him by preying on his fear for Myka’s life … which Myka and Lisa overhear.
Pete drags Paracelsus to be Bronzed, which restores history and changes the Warehouse back to normal … just in time for Artie and Claudia, and for Steve who was about to be killed by Paracelsus in the Warehouse. Back in the real Warehouse, Claudia says she has a weird feeling that things are changing … for good and bad. Maybe she was sensing the upcoming end of the series … 
yeah, there are only a few episodes left 🙁 Pete shows the others that he’s put both Bronzed Paracelsi (yes, there are two now) in an Egyptian sarcophagus, but Artie orders him to take them to the Bronze Sector. Myka asks Pete about what he said to Paracelsus and whether he had the scalpel because he thought it might cure her cancer. Pete admits it and Myka gives him shit, saying the Warehouse is supposed to come first. Pete isn’t sorry he did it, though. Claudia still wants to know about her sister being alive and Artie promises to tell her, even as he notes that one of the Versailles forks is missing. We soon see where the fork ended up … the evil Valda from the alternate reality has it, and it obviously allowed him to survive when reality was restored. That can’t be good.