Stiles: "He didn't tell you? It was in the tunnels, when Sebastien had his hands around Scott's throat. The guy probably didn't even know what he was doing. His claws got into Scoot's neck. He was going to kill him, but then he stopped and said a name-- Marie-Jeanne." Lydia: "He saw Scott's memories." Stiles: "He saw Allison." Lydia: "They must have looked like each other. I mean, maybe exactly like each other." Stiles: "It gave Scott a chance to break free. She saved him. Allison saved his life."
Scott receives the voicemails Kira left for him in The Beast of Beacon Hills in this episode, which eventually gives him the strength and determination he needs to rally the pack and finally defeat the Beast and Theo.
Deucalion reveals that not only has he been working with Scott and the McCall Pack since before Theo and the Chimera Pack tracked him down, but that he lied about his healed eyes being reverted back to their previously injured state, and he's actually had his eyesight this whole time as well.
This is especially ironic because in The Beast of Beacon Hills, Scott told Theo that he shouldn't trust Deucalion, which Theo took to mean that Scott believed Deucalion to be evil, when in reality, he was hinting that Deucalion would ultimately betray him due to his pre-arranged alliance with Scott.
Additionally, Deucalion reveals that Belasko's talons would have worked to take the Beast's power, and that what he told Hayden about them killing Theo was also a lie. This was confirmed when Malia uses them to take the rest of the Corinne's powers in this episode.
It is confirmed that shapeshifters with accelerated healing abilities can survive and heal from spinal injuries when Deucalion snaps Theo's neck and Theo survived the injury. This was previous implied to be true in Damnatio Memoriae, when Liam fell into the ravine and landed on a boulder so hard that he broke his back.
Chris Argent reveals to Gerard that he and Scott have also been working together this entire time, and that he knew that when he saved Gerard, that he'd only be concerned about immortalizing the Argent name rather than saving innocents from the Beast. Gerard was cured from his illness with yellow wolfsbane and brought back into the fold in Damnatio Memoriae.
Scott and Allison cuddling in Allison's car while they guarded Jackson (who was locked in a stolen prison van in the nature preserve to prevent him from attacking people in Kanima form) in Season 2's Frenemy.
When Stiles and Lydia discussed what happened with Sebastien seeing into Scott's mind, they realized that Allison and Marie-Jeanne must have looked exactly alike for Sebastien to have mistaken them. Marie-Jeanne first appeared in Maid of Gévaudan and was played by Crystal Reed for this exact reason.
Scott returns to the library to see the initials the packmates wrote during Senior Scribe on the bookshelf, which occurred in Creatures of the Night.
The episode ends with a scene at the shed where the Dread Doctors had hooked Mason up to the tank of green fluid. Since the Dread Doctors' death, Der Soldat (the Nazi soldier and Alpha Werewolf who fought in World War II) had no supervision and was able to escape from his tank, suggesting he will be part of Season 6.
The episode title, "Apotheosis," means, "the highest point in the development of something; a culmination or climax," according to Merriam-Webster's dictionary. An example is, "His appearance as Hamlet was the apotheosis of his career." The word "apotheosis" also means, "the elevation of someone to divine status; deification."
It is revealed that despite Tracy being a part-Werewolf, part-KanimaChimera, she does not possess the power of pain absorption like most Werewolves and Werewolf-Chimeras have.
Theo is dragged underground by his deceased sister, though it was not explained how she was able to do this. Theo's fate is also unknown, as it was not shown if he survived what his sister did to him or not.
This episode marks the last appearance of Arden Cho as Kira Yukimura, as she announced after this episode aired that she is leaving the show.