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Matheson had sacrificed herself in order to safe the Nightflyer. She felt that her death would break the feedback loop with Thale and allow him to communicate with the Volcryn and save the ship.
Lommie/Cynthia and Auggie meet below decks. She wants him to take the ship back home, and he wants to be with her. Murphy catches them talking closely.
Jhirl visits Captain Eris' broken body, strewn on the bed of his quarters. A projection of Cynthia appears to her and she runs to D'Branin to tell him about it. Just as she is telling him that Lommie didn't quite lock out young Cynthia in the ship's computer system, Lommie/Cynthia appears. She tells them that everything is fine and they don't need to worry about Cynthia, and that she wants to go back home. D'Branin encourages her to go into the memory sphere that he adapted with Volcryn organics.
In the memory sphere, (have we talked about what a great name that'd be for a band?) Lommie/Cynthia has a vision of Auggie disobeying her orders. She flips out, and starts tearing about the organic Volcryn material in the memory sphere. She believes that the ship is infected. D'Branin goes to talk to Rowan, believing that he might be the only one who can help Thale communicate with the Volcryn. Apparently all is forgiven on his recent murdering spree, and Rowan is suddenly back working with the team. He blames the nearness to the Volcryn ship. Seems like a horribly bad decision, but things aren't going well on the Nightflyer and D'Branin is desperate.
Jhirl heads back to Eris to try and talk to him again. He mutters something about a door, and she uses his eye to open a stealth door in the room and then enter the super secret chamber behind his bedroom. While Lommie/Cynthia tells Auggie she wants him to further sabotage the ship and then for the two of them to escape in a pod together.
D'Branin brings Rowan to Thale, and he is not happy to see him. After some coaxing, he agrees. He tells D'Branin that Cynthia has overtaken Lommie and wants to escape in a pod. And that if D'Branin wants to reach the Volcryn ship, he needs that pod to get to it. Murphy finds Auggie below decks sabotaging the ship, and confronts him. A fight ensues, and Auggie kills Murphy.
Jhirl finds some kind of version of Eris in stasis in the secret room, and Lommie/Cynthia tells her what's really going on. That, in truth, they are both genetically altered and should be considered brother and sister. Then she heads down to get into that pod.
D'Branin and Lommie/Cynthia fight over the pod, and he is able to get into it and escape. He is heading to the Volcryn. Lommie/Cynthia is furious. She heads back to Auggie to tell him, and he realizes that Lommie/Cynthia was going to leave without him. He tells security to lock her up.
Rowan and Jhirl, working together, want to save the Nightflyer. They ask Thale to find Lommie for her help, and Auggie is with them. He connects with Lommie's consciousness inside the computer system. They ask her to shut down the Nightflyer so that they can then restart it and save everyone on board. They then instruct all on board to huddle together in the mess hall to stay warm and fight to survive. Power shuts down across the ship.