“The Phantom Zone” begins with Brainiac overlooking Kandor. He mentions to himself that he thinks it’s time, and we see his massive ship start descending on the city.
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Lyta and General Zod are trying to find Seg among the rankless in Kandor, but things are too chaotic with everyone running around in a mass hysteria. Moments pass, and they’re able to locate Seg and Nyssa.
Seg and Nyssa inform the Zods that they saw Brainiac arrive. Zod begs Seg to take him to the Fortress; he wants to bring Val-El back.
We see a flashback to 14 years ago at Val-El’s sentencing. We see his assumed execution, but when he falls through the hole, he pushes a button on a handheld device and he’s teleported before he hits the ground.
The group arrives at the Fortress, where Zod explains that Val transported himself into The Phantom Zone. Zod reveals that when he was placed into the Phantom Zone in the future, he personally saw Val there. Zod mentions that somebody has to transport themselves to The Phantom Zone in order to retrieve Val-El.
Seg volunteers to go, but Zod tells the group that he’s the one that needs to go because he knows his way around the dimension. Val-El’s hologram beams Zod to The Phantom Zone, and Zod returns nearly instantaneously with Val-El. Val-El instantly recognizes his grandson, and the two hug.
Seg asks his grandfather for help defeating Brainiac, but Val-El says there isn’t a way to beat the villain.
Dev wakes up elsewhere with a new bionic arm.
The rankless are still frantically rushing about. Brainiac then begins speaking, and his voice can be heard everywhere in the city. Tentacles start expanding from his ship and attach themselves to the ground in Kandor.
We see Adam Strange has been transported to a planet that’s presumed to be Earth.
Zod tries convincing Seg to use Doomsday again, but Val-El speaks up and admits that the future in which they use Doomsday ends tragically for Krypton.
Dev walks into the Sagitari locker room, and most Sagitari soldiers refuse to take Dev-Em’s orders. Commander Garr tries to convince the others to flee, but Lyta walks in and confronts him about it.
Jax-Ur and the Black Zero are arming up for their fight.
Seg and Zod get back into the catacombs where Jayna was last seen. There, Zod reveals that they cannot let Brainiac see the future as some Kryptonians have. Zod recommends to Seg that they hand over Val-El as a peace offering of sorts, but Seg refuses.
Nyssa is in the Science Guild, retrieving the pod with her unborn child. She’s on her way out but is confronted by Jax-Ur, who blames Nyssa for the position Kandor is currently in.
Lyta is coming up with a strategy for the Sagitari in their fight against Brainiac. Seg is helping evacuate the rankless from the city when they look to the sky and notice the Sagitari starting an assault against Brainiac. The Sagitari ships are unable to get close before Brainiac hacks their systems and crashes all their ships.
Lyta tries to radio into all of the spaceship pilots, but none respond, hinting they’ve all been killed. Lyta’s starting to feel guilty about her actions and begins crying. Seg radios in to make sure she’s safe and she responds.
Nyssa and Jax-Ur are walking out of the Science Guild when Jax-Ur asks Nyssa if she remembers when her mother died. Jax-Ur reveals that Nyssa was with her mother when she died, and hints at the possibility that this version of Nyssa is a clone.
Seg and Zod are still helping evacuate the rankless when Zod decides he’s going to give Val-El to Brainiac. Zod enters Brainiac’s building and confronts the villain. There, Zod offers Val-El up to Brainiac, but Brainiac begins choking him to find out if his offer is legitimate.
Upon finding out Zod’s offer is sincere, Brainiac asks what Zod wants in exchange. Zod reveals that he’ll let Brainiac control the rest of the universe in exchange for control over Krypton.
Lyta’s trying to run down Dev among the rankless when all of the rankless freeze.
Zod takes Brainiac to the Fortress of Solitude, where he confronts Seg and Val-El. Seg tells Zod and Brainiac that he’d rather kill his own grandfather than hand him over to Brainiac.
Brainiac uses his powers to stop Seg from shooting Val-El. With Brainiac on the platform at the Fortress, Seg triggers the portal to the Phantom Zone. Brainiac is sucked into the Phantom Zone, but his tentacle extends out and sucks Seg in with him. Val-El tries to stop Brainiac from taking his grandson, but Seg notices that Superman’s cape has restored in full, signifying the future is fixed. Seg lets go.
Brainiac’s army and ships cease working. Val-El tries to open the portal again to bring Seg back, but Zod shoots the panel, destroying it and ruining the way for Seg to get back.
We jump into the future one month and see that Zod has assumed control of Krypton. He has turned the rankless into members of the Sagitari and is ruling the planet as an authoritarian leader. The logo on Superman’s cape turns into Zod’s emblem.
On Earth, Adam Strange notices a statue of Zod has been erected.
The episode ends with Doomsday waking up and breaking out of his pod.