As Clarke uses the Red Sun Rising book to draw connections between the "red sun" eclipse and Emori's sudden psychotic behavior, a flashback shows the first time the original Eligius III space explorers first experienced the phenomenon:
- It was 236 years ago and the Eligius III's Mission Team Alpha astronomers had just recently landed on the Alpha moon. A young taxonomy scientist named Josephine Lightbourne when she noticed the approaching eclipse and started taking photos. She came back inside where her father reminded her to remain focused on their mission because they were building a sanctuary for human race. Because of the safe, peaceful nature of the place, Josephine suggested naming it "Sanctum," the Latin-root of "sanctuary." Josephine then went back outside and started making out with her boyfriend under the red sun. She then realized that something wasn't right because all the insects had gone quiet. Because of her deep understanding of eclipse on animal behavior, she anticipated a swarm of bugs. They started driving towards the outpost with motorcycles for shelter only to find that her father had turned psychotic and turned against his wife. Mr. Lightbourne started shooting everyone including his daughter, Josie, shouting, "Sanctum is mine!"
In the present, Clarke explains to her friends that the "Red Sun Rising" book shows that the eclipse turned Emori against the rest of the group. Since they're likely to turn as well, the group agrees to handcuff themselves until the danger passes. They agree to use different areas of the village just in case - Clarke with Bellamy and Murphy; Echo with Emori; and Miller with Jackson. Bellamy decides to keep all the keys. This causes Murphy to escalate his complaints against Clarke's betrayal and how she and Bellamy have hurt him countless times throughout the years. He calms down when Clarke takes Bellamy's keys and admits that she is not a good person and whenever she leads, people get hurt.
Before long, the trio hears banging and screaming from Miller and Jackson's cabin. Clarke and Bellamy go to check it out. They find that Miller has turned into the psychosis state and is hallucinating. They unchain Jackson so he can help Miller. Soon, Jackson too, turns psycotic and grabs a knife. Bellamy sees and tries to stop him. Jackson shoves away Bellamy and stabs Miller's arm. After trying unsuccessfully to calm Jackson down, they knock him and Miller out with a tranquilizer. Returning to their cabin, they find that Murphy has broken free and has taken all the guns. They go to warn Echo and Emori. Emori taunts Echo as well as a voice she keeps hearing. Soon enough, Echo tranq's herself. As Bellamy violently bangs on the door, Clarke realizes that Bellamy has turned too. Murphy fires his gun at Bellamy and Clarke, making them run in different directions.
While hiding from Bellamy, Clarke starts hallucinating too. In the hallucination, Abby "calls" Clarke on the radio and tells her that the only way to prevent the harm she's done to her friends is to kill herself. Murphy enters the room and finds Clarke with a knife to her throat. He persuades her to put the knife down. Murphy mentions that the radio is off. That calms Clarke. Since she is only threat to herself and won't harm him, Murphy suggests they should pair up and stop Bellamy together. It doesn't take long before Bellamy gets a hold of Murphy and tries to drown him in a pond. Clarke again hallucinates hearing her mother's voice. She manages to overcome the taunting and stops Bellamy from harming Murphy. Then Bellamy starts to choke Murphy. Clarke takes out a gas genade and pulls the trigger and knocks them all out.
Back in the mothership, Octavia is angrily training with a reluctant Niylah. She's so angry that she punches a control box several times, causing her wrists to bleed. Her training is interrupted when the Gagarin suddenly returns. They go in to check why their friends on the ground returned so soon. It turns out, the transport ship was hijacked. The four hijackers are wearing black suits and gas masks. They drop gas grenades, knocking out everyone in sight, before locking them all in the mess hall.
Luckily, Raven is in the cryo room. She quickly wakes up Diyoza and explains the situation. Diyoza comes up with a plan where she pretends to be asleep while two other intruders enter the chamber. She quickly grabs one of the hijacker's guns and kills both intruders instantly. She takes one of their radios to make demands to their leader on the other end, a woman named Kaylee. Since Kaylee doesn't know her family are dead, Diyoza uses them as leverage. Kaylee agrees to let everyone free if Diyoza sends her husband back to her on the bridge. Since Diyoza has already killed them, she convinces Raven to put on the suit and pretend to be Kaylee's husband.
After regaining consciousness in the mess hall, Octavia impatiently starts hitting the doors, trying to get out, despite everyone else telling her that there's no way out. She feels like it's her responsibility to save her people again. Abby reminds her that everyone still hates her for what she did in the bunker and warns her that everyone in the mess hall are from the Ark, who lost their loved ones in Praimfaya. Octavia blames Abby for cannibalism and for the fighting pit. She says that she would have brought Wonkru safely to the valley if it weren't for Kane and Abby's betrayals. As Octavia adamantly insists that she's not to blame for anything, everyone gets irritated with her insults. Fed up with her sadistic behavior, some of the people in the room including James, who lost his mother in the massacre in the gorge, become angry at her. This causes a fight between Octavia and Sky People. As she understands their anger, Niylah asks Abby to intervene but Abby just watches. James puts a knife on Octavia's throat and declares the queen dead. Octavia dares him to kill her but Abby finally intervenes and tells them to leave Octavia alive with that burden. Octavia breaks down and starts crying, begging them to kill her.
At the bridge, Diyoza brings Raven in disguise to the intruder's leader. Kaylee notices a bullet hole on the suit and therefore is not convinced that it is her husband and demands that they take off the mask. As a fight breaks out, Madi jumps down from the vent and joins in. The other member of Kaylee's gang (Faye) gets shot in the mix and bleeds black blood. Madi points out that she is a nightblood. She then asks Raven for Clarke's whereabouts. After losing her sister, Kaylee surrenders and explains the situation they were fleeing on the ground. They agree to go back to the surface as the eclipse passes.
Upon landing, the group notices that Octavia has joined them as a stowaway. She refuses to go back and says she's there to save her brother. Madi wants to go with them too, but Abby asks her to stay behind in the transport with Diyoza and Gaia. Diyoza agrees, knowing that if their dropship is hijacked again, they're screwed. This leaves Raven, Octavia, Jordan, and Abby to save their friends. Octavia leads the way after quickly figuring out where their friends went. As they approach the radiation shield tower outside Sanctum, Kaylee warns them about the radiation. Since she's a nightblood, Kaylee is unaffected. She goes through the gates and notices Shaw's grave. When she asks the group who Shaw is, Raven breaks down in tears. Kaylee reluctantly enters the code into the control box on one of the towers.
The group continues their journey towards inside Sanctum, where they find Clarke, Bellamy and Murphy all passed out. They wake them up but Murphy is too weak, with noticeable black lines growing under his skin. However, before getting all the answers, they're interrupted by noises from a group of children approaching the castle. One of the children, a girl named Rose, asks if they've come to take them home. Clarke says, to them, "Isn't this your home?"