With over 50% of the Resistance's ground forces wiped out, General Zod is pleased, but surprised to find Seg-El standing behind him with a pistol. He approaches, and is pistol-whipped by Seg and held at gunpoint. Seg taunts Dru, saying he should have expected this, but Dru asserts that no one in history has been able to withstand a Somatic Reconditioning. Demanding to know how Seg did it, Brainiac appears beside Seg and advises him not to answer truthfully, and although Seg looks at him, Zod cannot see him; he exists only in Seg's mind. Despite the stream of advice from Brainiac, Seg tells the air to "shut up", appearing to General Zod to be talking to himself, before Seg orders Zod to undo the damage to Lyta's mind.
On Wegthor, Lyta informs the Rebel task force that their ground support are all dead and that "this war is over". However, despite Kem's protestations, Adam Strange tries to get Lyta's attention as "Seg's buddy", but she remembers him as "the one who wanted him to kill our son and let Brainiac take Kandor", at which point Kem and Araame glance pointedly at Adam. They steal Adam's Zeta Beam, but then release Araame and the rest of the task force (but not Kem and Adam) as a "sign of good faith", provided that they bring a message back to Jax-Ur and Val-El that Lyta requests a meeting to discuss surrender.
Val and Jax meanwhile argue about Jax's use of a genetic weapon, arguing that it is immoral while Jax argues that they had been betrayed, making it necessary, as Nyssa-Vex arrives at the base station to report back to General Zod, only then realizing that the information she fed to the Rebels resulted in them all dying of tainted oxygenators. Lyta arrives and congratulates Nyssa for finally choosing the "right" side. Araame also informs Jax and Val of Lyta's request, Lyta placing her faith in Val not to let Adam or Kem come to harm as her hostages, and in New Lurvan Jayna-Zod and Dev-Em try and fail to recruit people to their cause against General Zod.
In Kandor, Seg tells Zod that they never were or will be a family, and then begins interrogating him as they cannot yet contact Lyta due to a solar flare. On Wegthor, Val insists on meeting Lyta, but Jax objects because they tried that in Bokos only for Lyta to gouge out Jax's right eye. Val insists that Seg can get Lyta to come around and reveal Zod's use of Somatic Reconditioning, despite the risk, and so Jax agrees. Meanwhile, Adam and Seg are being processed while Lyta assures Nyssa that she will soon have her son back.
En route to Kandor via skimmer, Jayna-Zod asks Dev-Em why he didn't join the Resistance. He considered it, but Jax-Ur had been in charge of Black Zero, who killed his family, and so he couldn't stomach it. He professes not to know "which side" is right anymore, being faithful only to Jayna.
Again in Kandor, General Zod insists that he only Somatically Reconditioned Lyta to take away her guilt and pain from her shooting her mother Jayna, and loneliness at Seg's absence. Seg accuses Zod of taking away the best part of Lyta, her empathy, and continues that once she knows the truth she'll turn against Zod. Zod however believes that she will choose him over Seg just as she did him over her mother.
At the summit between Lyta, Jax, Val, and Araame, Lyta insists on "complete surrender". She says that no one will be killed, and every Rebel would be assigned to different Guilds, Jax and Val going to the Science Guild in particular. Further, she has snipers placed all around the area to ensure their cooperation, and Kem and Adam will only be safe if they agree to her terms, also saying that although there will be casualties on both sides she is perfectly capable of crushing the Resistance. Val tries to reason with her using Seg's name, but Lyta says that Seg is with General Zod, and is unmoved. She insists on a decision, but Jax screams "no deal" as a hidden laser beam within her replacement eye activates, slicing through the snipers. Jax then assaults and captures Lyta, to be used as a hostage due to General Zod's love for her.
When Seg orders Zod to contact Lyta, he only sees Jax's face, who presents Lyta as a hostage before all of Kandor. While Seg is distracted by the tableau, Zod disarms Seg and holds the pistol to Seg's head. Jax explains to the people of Kandor that Zod was reconditioning people, gives Zod one hour to withdraw his troops from Wegthor, otherwise she will kill Lyta. Val objects, so Jax has him taken into custody.
Jayna-Zod and Dev-Em arrive in the Military Guild, noticing that Zod's fleet is mobilizing to ascend to Wegthor. They are apprehended but manage to convince the Sagitari officer to grant them access to General Zod's chambers. General Zod himself contacts Jax-Ur and agrees to withdraw from Wegthor, then ordering his Sagitari to depart the moon in an obvious way so that the rebels can notice it. He then asks Seg if he still doubts that he will do anything to protect Lyta, who still does, before Zod says that all he ever needed from his father was for him to be proud of Zod. Although Seg says they can talk, Zod cuts him off, saying that that was in the past; he no longer needs that, or anything else from Seg, and then Zod knocks Seg out cold.
As a Sagitari is messing around with Adam's Zeta Beam, Nyssa-Vex arrives and shoots him, freeing Adam and Kem. Meanwhile as the retreat continues, Zod asks only that he be able to see Lyta, and at the same time Jayna and Dev kill Zod's guards to gain access to his chambers. Adam and Kem however have discovered several bio signatures in an area of tunnel where there should be no one there, and so they rush back to Val.
Zod requests that Jax allow Lyta to speak with him, which she accepts on the condition that no coded language is used. Lyta insists that she is willing to die for the cause, but Zod says "I am not willing to let you die", at which point time seems to stop and Brainiac appears, asking Seg whether he believes Zod. Brainiac comments that Zod is "quite a formidable liar", and when Seg asks whether Brainiac has returned, he says that he never left, and that he was able to protect Seg from the Somatic Reconditioning. He then counsels Seg to warn Lyta of the reconditioning and to kill Zod.
Seg attempts to do so but is prevented when Zod turns off the connection. They then fight and Zod strangles Seg until Dev and Jayna arrive, Zod using Seg as a human shield despite Seg pleading with Jayna to take the shot. Zod remarks that she can’t do it, at which point Dev says "no, but I can" can prepares to shoot, at which point Zod throws a knife at Jayna's face, forcing Dev to grab it out of the air while Zod escapes for help. Dev, Jayna, and Seg then flee.
With the Resistance, Jax is concerned that the connection cut out despite the retreat continuing as agreed, so she orders Lyta to be returned to her cell. Meanwhile, Seg escapes using Brainiac's stream of advice, telling him exactly where each Sagitari will be so that Seg can shoot them before they even realize what is happening. He then trains his gun seemingly right on Jayna's face, until another Sagitari enters behind her who he shoots.
Adam and Kem deliver their findings to Jax, Val not being present, as Seg and company head to the old Rankless District to hide in the underground rebel network there. Adam's findings turn out to be an encampment of Sagitari lying in ambush, the ones heading to he Space Elevator having been fakes, and so Jax publicly calls Zod a liar. Preparing to cut open Lyta's throat on camera, Val-El is heard pleading desperately with Jax not to do it, not to become like Zod, and although Jax hesitates, she cuts Lyta's throat anyway for all to see.