After Octavia's departure, Bellamy is kidnapped by invisible figures while Hope shows no memory. Gabriel, Hope and Echo chase after Bellamy's kidnappers; after experiencing a hallucination of Roan and the real Echo, Echo kills three of them. With the Anomaly closing, Gabriel, Echo and Hope choose to follow the others through it to find Bellamy.
With the various factions now living together in Sanctum, tensions rise, particularly with the Children of Gabriel demanding Russell's execution while Murphy is guilt-stricken over his role in Abby's death and Madi continues to experience memories from one or more of the Commanders.
A depressed and suicidal Russell destroys Priya's Mind Drive and goads Clarke into killing him; after Clarke knocks Russell unconscious, he is greeted by Sheidheda in the Mindspace who had uploaded himself into Russell's Mind Drive when the Flame was destroyed. The Dark Commander kills Russell and resurrects himself in Russell's body. Unaware of this, Clarke burns down the Sanctum palace and announces a new beginning for Sanctum and that "Russell" will be executed the next day for his crimes.
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Clarke Griffin: "Sanctum is free! There are no kings or queens or Primes here. We have no use for a palace. We are the last of the human race, and we've all made mistakes. Tomorrow, Russell Prime dies for his."
It's stated that there are currently 36 Eligius IV prisoners still alive in Sanctum, but Diyoza went missing on another planet.
After Indra states that the problem in Sanctum is "too many people," Raven quips that it's a "good thing A.L.I.E.'s not around." This is a reference to the fact that A.L.I.E. started the Nuclear Apocalypse because she felt the problem was "too many people."
Amongst Madi's drawings are the Ark and Polis. Though Gaia questions the origin of her drawings, Madi states that she doesn't know why she did aside from being bored in school. Gaia later shows Clarke the drawings and states that Madi is drawing memories that are not her own. Though Clarke asks if its Sheidheda, Gaia suggests it could be any of the Commanders or all of them.
As seen in the HUD of one of the people Echo shot, they are from Bardo.
It's revealed that Kaylee Lee stopped Oblation after Josephine Lightbourne VII's death, inspired by her Null lover Isaac who caused Kaylee to see what the Primes had become.
The fate of the other Commanders currently remains unknown, especially since Gaia suggests that Madi might be experiencing their memories.
The reason that it took so long for Sheidheda to take control is that Russell had to be asleep or unconscious for them to be in the Mindspace together as seen with Clarke and Josephine. Russell had been refusing to eat, drink or sleep since his arrest.
In the same interview, Jason explained that when Sheidheda uploaded himself when the Flame was destroyed, the code went into the ether of the system WiFi on the ship where it eventually found its way into Russell's Mind Drive.
It is revealed that Jordan Green is not brainwashed and still does not believe in the Primes, but instead saw a vision of the Temporal Anomaly.