Synopsis of 03×02: The Librarians are forced to face Anubis and his army of werewolves when a rip in time and space is opened and Apep brings them through. Charlene makes an appearance and it is revealed that she was the original guardian and may be the only person who can help defeat Apep.
They found Charlene in the temple surrounded by what had previously been a dangerous cult. According to her, she used an enchantment artifact to trick the men into thinking she was a goddess, and reaped the benefits of their endless attention. Charlene seemed reluctant to return to the Annex to help Flynn and the rest of the team until they mentioned Apep and she realized how serious the situation truly was. She insisted that they would rest that evening and head out first thing in the morning.
Naturally, Flynn and Eve took the time to relax together and discussed what it would be like to take a real vacation for once instead of always being wrapped up in the insanity of their tasks.
When they got ready to go the next morning they found the temple in ruins and Charlene’s merry band of men apparently dead at each other’s hands. Charlene was nowhere to be found. It became clear that Apep had been behind it and Flynn immediately made it his task to locate her.
They returned to the Library where Flynn tried to reprogram the door to specifically find Charlene, despite Jenkins’ protests that the door was meant to find places not people. He then became cross when one of the Librarians referred to Charlene as an accountant and claimed she was an important figure because she was the guardian to the first Librarian.
Flynn’s attempt to reprogram the door worked and everyone got through except Eve who was left behind with Jenkins when the door collapsed unexpectedly. The rest of the Librarians ended up in a Super Collider facility after an explosion sent it into chaos and left weird half-men, half-wolves roaming the halls. Jenkins managed to get the door to send him and Eve to the general area, but they were stuck trekking through the woods to try and unite with the rest of the team.
The Librarians met up with the remaining non-werewolf staff and began to piece together what had happened. With what little video footage they were able to get, Flynn believed that Charlene had been at the heart of the explosion and fretted that she was dead. He became nearly fixated on her status and put the team at risk as he insisted they had to find the remains and verify that she was really gone. Flynn ran out the door and Jake was forced to follow him.
Jenkins and Eve approached the outskirts of the facility and met the nicest gate guard in the world who immediately offered to help them to the facility after Eve pretended they were there on official business. Inside, the Librarians and the remaining staff at the facility tried to get a handle on the situation. Flynn found Charlene’s pendant but did not find her remains. They determined that Apep may have possessed her to try and kill her, as well as use her to rip open space and time to pull Anubis and his werewolf crew through.
As a result of the team’s attempts, Ezekiel was bitten and not doing well. Flynn realized that they had been tricked into coming to the facility by Apep, who intended to have them killed by the werewolves. He had been so fixated on Charlene that he neglected to take precautions to see the bigger picture, and as such had put his team – and Ezekiel – at risk.
Eve wanted to know why Jenkins had accompanied her, considering his general distaste for leaving the library. He told her it was because he was worried about Charlene, the Librarians, and the situation as a whole. It was at that point the gate guard mentioned specifically that she would help them with their friends, and Eve realized the guard had been possessed by Apep. Apep had led them off track because he wanted to figure out if his trap had worked, and now that he knew it had he planned to go watch the Librarians die.
Jenkins saved Eve by pulling her off a cliff and using his own (immortal) body to cushion the fall. Meanwhile, Flynn was useless and upset inside, consumed by his own guilt and worry over how he tended to put people in danger. During his pity party, one of the staff set the facility to self-destruct in the hope that it would end the chaos. The rest of the team pulled it together and Ezekiel offered to be a distraction in order to allow the other Librarians to shut off the power and stop the self-destruct from occurring.
As Jenkins and Eve followed Apep from a distance, Jenkins finally disclosed the narrative regarding the final battle and Charlene’s role in it.
Back in the facility, Ezekiel managed to act as a distraction and due to changing partially into a werewolf was accepted by Anubis and his crew while the rest of the team took up positions. Flynn acted to lure Anubis back toward the portal, and Eve and Jenkins finally made it into the facility to join them.
With a bit of work the portal was opened and they sent Anubis into it, and Apep gave up possession of the guard. On top of it all they stopped the self-destruction and managed to kind-of save the day, even though a lot of people died.
Flynn was still lamenting his role in all of the destruction when Cassandra admitted to using magic to fill out the video from earlier. They realized that it had not been Charlene in the explosion but another woman who looked similar enough, but was clearly someone else.
Apep just wanted Flynn to think it was Charlene to lure him in, when the real Charlene managed to get away. Flynn left the team to go find her, leaving Eve a sad note about how he was going to keep his distance for now in order to protect the people he cared about most.