"Zods and Monsters" opens with General Zod giving a speech to Kandor, acknowledging the death of his mother, but brandishing a new weapon; Doomsday, who Zod claims is now within Zod's control and aimed at Wegthor in vengeance. Zod's first fleet of ships are also complete, and Kandorians cheer.
In a skimmer moving through the Outlands, Nyssa-Vex offers to listen to Seg-El about Lyta-Zod's loss. Seg remains quiet however, and Nyssa asks where they are going, Brainiac asking as well. Seg says he cannot say, asking Nyssa to trust him, and Nyssa clues in that he is trying to hide the knowledge from Brainiac, even though Brainiac says he can hear Seg's thoughts. Seg, reneging on the deal he made with Brainiac, says that he intends to get Brainiac out of him and not to take him anywhere near his Skull Ship, but Brainiac causes Seg to freeze and stop talking. Nyssa takes control of the skimmer, and Seg grates out "fortress", which Nyssa understands and begins going that way.
Val-El on Wegthor plans to oust the remaining Sagitari forces, assigning Kem to the task of leading a mission to accomplish it. Adam joins Kem, with Kem humorously forcing Adam to ask permission to do so, and then describing in detail the horrors of radiation poisoning, before departing. By this time Nyssa has arrived at the Fortress of Solitude, conveniently abandoned by General Zod, with Seg in tow. Val-El's hologram appears, offering assistance, and although Seg asks to hold his son one last time, he collapses as Brainiac takes complete control of his body.
In Kandor, General Zod is attempting to gain complete control of Doomsday, having only actually managed to "deactivate" him. Time flashes back, to 1,000 years ago, where Els and Zods were creating Doomsday, using a man named Dax to create him, as Dax has the correct Vara gene they need to accomplish the transformation. Dax talks with his wife, Enaj, who does not want Dax to sacrifice himself, but Dax insists that it must be done to end the war, and says his goodbyes to not only his wife, pressing his finger against the glass in mirror to hers. Although he promises to come home, Wedna-El tells Enaj to tell their daughter that Dax is helpng to build "a better tomorrow", so that she may grow up on a peaceful Krypton free from civil wars, and Enaj departs. Van-Zod then has Dax position himself in the center of a chamber, and together with Wedna, they plan to enhance Dax, to make him invulnerable to all lethal force, into a "superhero" as Dax puts it. They begin the transformation.
Back in the present, Kem and Adam are entering the mines on Wegthor. Kem sends both of his teams away on separate tasks while he and Adam move on, Adam complimenting Kem on how much he's grown from being a bartender to an efficient soldier. One of his soldiers informs him that they've found the Sagitari, suggesting immediate attack and dissuading Kem from doing reconnaissance, but Kem insists on it, and they press on.
In the Fortress of Solitude, Val-El's hologram discovers Brainiac to be clustered around Seg's brain stem. On Seg's orders, he begins the process of removing Brainiac, only for Seg to destroy the machine when Brainiac makes him do so. Seg has Val's hologram restrain him, and then the hologram tutors Nyssa-Vex on how to do the procedure manually. Although Nyssa balks, Seg talks her into doing it anyway. While she works, Seg sarcastically mentions that if she fails then he'll be too brain damaged to care much, which Val-El's hologram finally gets is sarcasm.
General Zod's scientists are having difficulty accessing Doomsday's brain in Kandor, much to General Zod's frustration. Although his lead scientist urges caution, that going too quickly could impair Doomsday's ability to process, Zod again does not care and orders her to press on. She locates a memory, one of trauma, and Zod orders her to show it, once again showing the time from 1,000 years ago. Wedna and Van continue to torture Dax/Doomsday until he dies, and then resurrect him afterward and administer the same torture, which he is now immune to. They then move on to another torture, fire, which kills him again, and again they resurrect him, now immune to flame.
The cycle of torture continues through 105 tests, with Dax now no longer recognizable as human, his body having adapted to all manner of extreme environments. Van-Zod eventually loses his stomach, and tries to stop Wedna-El from continuing, arguing that it is wrong, but Wedna insists that it must be done in order to save Argo City from the Kandorians, and they continue torturing and resurrecting Dax.
Once more in the present, Nyssa seemingly successfully completes the procedure, and after Seg finally holds his son with a clear mind, they decide to rename Cor-Vex to Jor-El, after Val's father. In the Wegthorian tunnels however, Kem's reconnaissance comes up with "something", but not necessarily the hostiles. He subordinates, including Adam, insist that he attack immediately lest they lose the advantage, and when Kem insists on doing further reconnaissance one of his lieutenants storms off. Adam tries to reason with Kem, but Kem asks Adam to have some faith and stay put, before continuing on.
In the chamber with Doomsday, General Zod dismisses his lead scientist, who reluctantly departs. Using his knowledge of Doomsday's memories, he speaks to Doomsday, calling him a hero, saying they are brothers in protecting "Mother Krypton" at all costs and that Doomsday will fulfill his destiny to do so. At that moment, time flashes back again to 1,000 years ago, where Wedna-El and Van-Zod are at trial 455. While in procedure, Enaj barges into the room and pulls a gun on them both, saying that Jo-Mon has ended the war and that they have no need to keep her husband any longer, demanding he be returned to her. Wedna refuses, saying there will always be another civil war, and that her husband can prevent it if she finishes perfecting him. She tells Enaj to go ahead and shoot her, or else let her continue her work, and Enaj is just about to pull the trigger when she hears Dax inside the testing chamber.
Enaj rushes to the window, calling for Dax, but Wedna says "he's not your husband anymore". Enaj demands to know what they did to him, and Van-Zod says that the Zods and the Els have failed her. At this point, Dax, now fully Doomsday, arrives at the window, and like before, he puts his finger on the glass for Enaj to mirror. Enaj is horrified however, and runs away, sending Doomsday into a rage as he bangs on the glass of his enclosure. Snapping back to the present, General Zod speaks Enaj's name, waking Doomsday.
In the Fortress of Solitude, Val's hologram notices that Brainiac's Nanites are gone. Meanwhile, Kem's lieutenant nearly commits insubordination, but Adam Strange stalls until Kem arrives. When Kem orders the unresponsive soldiers to give the people he brought with him, starved and stellarium-addled Sagitari, their lunches, Adam backs Kem up and gets them into motion. Together with their squad, they bring the Sagitari to Val, who congratulates them on a job well done.
Again in the Fortress of Solitude, they are unable to locate Brainiac's Nanites despite scanning the Fortress three time. The hologram of Val scans Nyssa and Jor-El, and is about to scan Seg, until the hologram glitches out and Brainiac takes over the system in the Fortress. In Kandor, Brainiac's Skull Ship activates and begins to rise, shocking General Zod as he sits with a glass of liqueur. He rushes down and orders the skimmers to scramble, but everyone is in motionless shock.
In the Fortress, Brainiac says that, had Seg kept his end of the bargain, this could have been avoided. He would indeed have honored his end and departed, as his designs no longer involve Kandor City at all. Seg disbelieves him, but brainiac says "that is of no consequence", before the roof is blasted in by his ship. Preparing to depart, Brainiac offers Seg the chance to join him for one last time, but again Seg refuses, saying that Brainiac doesn't understand him if he thinks Seg craves to destroy as Brainiac does. Brainiac fires back that it is Seg who does not understand him, that he only wishes to preserve unique cultures, saving them from self-destructive impulses, but Seg only says that Brainiac is a self deluded monster who sees himself as a god, and that he will never join him.
Brainiac comments that Seg's choice is "as illogical as it is disappointing", but that Seg has "earned the right to make it", and bids Seg farewell, leaving him in peace and vanishing. As he does however, his voice reverberates throughout the Fortress:
- "My directive is as it always was--to preserve the best of Krypton. I once believed it was Kandor City. Now I believe that the best of Krypton lies within the blood of the Els."
Jor-El vanishes, beamed up to Brainiac's ship, and Nyssa becomes hysterical as Seg restrains her, screaming "you said this wouldn't happen!". Everyone in Kandor then watches is awe as Brainiac's Skull Ship powers up, and vanishes.