The episode begins at the Metropolis Institute of Technology, where John Henry Irons waits anxiously for something. He re-enters his RV, greeted by his AI, and they set out for a woman’s residence. As he’s watching this world’s version of his sister, Lois calls him back to Smallville to help.
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At Rho’s lair, Superman is fighting the influence of the Eradicator. After a rant, Tal-Rho tells him that he is to be replaced with Zod, and resistance to Zod’s will is futile.
Back at the Kent Farm, the boys are worried, and Lois tells them that Clark is doing to be OK. They don’t believe her, but she’s speaking from experience, and tells them to go to sleep and stop worrying. As they leave for their room, Sam pulls up outside. He asks the location of the Fortress, and Lois tells her father Clark isn’t there, and that Rho’s Fortress is in the desert. As Sam is adjusting the DOD’s search grid, Lois finally breaks down in tears.
At the Cushing house, Kyle is annoyed by having to go check in with the military and be quizzed about his experiences with the Kryptonians. His doorbell rings, and it’s one of his firefighters. She says the rest of the crew doesn’t want him there, because he vouched for Edge. she suggests that he takes a few days and gives people a chance to cool off.
At the Kent farm, Jordan and Jonathan are frustrated that the military can’t do anything to find Clark. Jon suggests that Jordan could use his super-hearing to try and track down Clark. Jordan resists it, but Jon coaches him to figuring it out.
John Henry discusses what happened with Lois, and while he admires that Superman surrendered to protect her, and asked her to call John in, he says that if Superman is sending for him, even Superman knows the only choice is to kill Superman.
Lois tells John that she won’t let him kill Superman, and John asks why she thinks Superman isn’t trying to sacrifice himself. Lois tells John that she will prove to him that Superman won’t be turned. She storms off, and Sam and John start strategizing for if it becomes necessary to kill the Kryptonians.
Outside, Jordan is worried about not being good enough to find Clark, or to help if he does, but Jon tells him that what happened when Clark surrendered himself isn’t his fault, and that Jordan can help now.
In the RV, John reveals that he and the Lex Luthor of his world created a sophisticated missile based on red sun technology that can completely deplete a Kryptonian’s power for long enough to kill them. He tells Sam to build it, and if John Henry has it, he will figure out how to use it, even without his ship.
In the town square, Emily and her family confront the Cushings about their role in getting her eradicated. Lois tries to encourage them that they won’t be held accoutnable forever, since it isn’t their fault. He calls them into the newspaper to ask them what they remember about being a Subjekt. Lana has nothing to say, but Kyle has more memories, since he was fighting the influence. He tells Lois that he felt like he was losing himself, he couldn’t remember things, and it hurt. He said that no matter how he fought, there was an overwhelming sense that his family would be better off if he let go, and he almost did. Lois’s big takeaway is that you can fight the influence.
In the desert, that’s what Superman is doing while the two Rhos look on. Superman remembers his family and flies off at top speed, but crashes into the rocks outside of Rho’s Fortress. Back in Smallville, Jordan hears Clark calling him.
The two are calling back and forth between one another, and Rho interrupts to tell Jordan not to send anyone after him.
Diggle is in the town square, having provided some tech for Sam and John Henry’s missile. Lois finds out, and she’s infuriated that Sam lied to her. Diggle is angry, too, that Sam lied to him and Lyla about what the tech was for. He’s also not thrilled that Sam was harboring someone from another Earth without disclosing it.
At the Cushing house, Kyle freaks out after he returns to find one of his windows broken out and graffiti on the building telling them to get out of Smallville. After a tense few minutes, Lana and Sarah go inside, while Kyle goes to start cleaning up the house.
After the boys tell Sam about what they’ve learned, he tells Lois that when they locate Rho’s Fortress, he’s sending in John Henry with the missile.
Lois pulls John Henry aside and tearfully admits to him that Superman is her husband. This obviously shakes John Henry somewhat.
She admits that the boys didn’t know who Clark was until this year, and that’s why they moved to Smallville. She tells John Henry that things are different here, because he has more to fight for than he did on John Henry’s planet. John isn’t impressed. He tells Lois that he has a responsibility to do the right thing, and he’s not going to be influenced by her tears.
Diggle tells Sam that he’s done with the life he lived during his years with Oliver, but that he’s disappointed in Sam and John Henry for not exhausting all options to save an ally and a hero.
Back at the Cushing house, Lana and Sarah are having trouble getting the paint off the house. Kyle shows up with some paint thinner to help out. The trio end up in a water fight with the hose and cleaning supplies, giving them the first happy moment as a family they’ve had since all of this started.
At the Smallville Register, Lois is getting herself together when the boys come in. They ask if they’re too late, and she says she doesn’t know.
In the desert, Superman collapses, and Rho starts gloating to his holo-dad about it. Superman stands before them and talks in a creepy, disembodied voice — he’s talking to them as Zod.
Just then, Sam and John Henry find the desert Fortress. John goes to do a final system check, and Jonathan confronts him, trying one last time to get through to him not to kill Clark. John Henry tells him he wishes there was another way, and Jon tells him there’s always another way.
In the desert, John Henry flies in, armored up and carrying his hammer.Superman flies to him, his eyes glowing, and attacks.
As in the pilot, Superman and the armored John Henry fight in space, then fall back to Earth. Sam authorizes him to use the missile against Superman, but Lois counters that if he does, they have nothing to fight Edge with. She says John Henry has to get through to Clark and make him remember who he is. As she says this, Superman has a flash of humanity, and John Henry uses the moment to clock him a few times with the hammer.
Clark starts to stand back up, and tells John Henry that he has to kill him, and that he can’t stop. He tells John to kill him to save the world, and that’s what makes John decide to talk to him as a man instead. He calls him Clark and tells him that his family believes in him. He shares his experience , and he tells him that the pain he’s feeling right now is nothing compared to what he will feel if he loses Lois and the kids. With visions of all of last week’s flashbacks, Clark screams and falls to the ground, having seemingly flushed Zod from his system. John helps him to his feet, and radios in that Clark is back. He tells Lois he will be back soon, but first, he and John Henry have to deal with Rho.
Back in his cave, Rho tells his father that Zod has been turned back. his father tells him “it’s time,” and that he wants his son to go and complete what he was sent to do. Rho blasts through the wall, carrying the Eradicator, and flies off at top speed. Superman and John Henry give chase, but it’s hard to keep Edge in range when he goes straight up into space. He’s preparing to overload the Eradicator with his heat vision, presumably to reverse what Clark did last time, but the missile catches up with him and he plunges to Earth. He starts ranting at Superman, who punches him out.
At the Kent Farm, Lois tells the boys that she knows how they’re feeling, and it’s the worst, but Clark will be home. Jordan hears him coming first, and they all scramble out to meet him. Moments later, John Henry falls from the sky, his hammer in hand, and introduces himself formally to the family. Lois invites him over for dinner, but John has to go wrap things up with Sam. He takes the hammer and blasts back off, leaving the family to have their alone time.
At the Cushing house, Sophie comes home from Lana’s mom and there’s a happy family reunion.
At the Kent farmhouse, Sam tells Clark and Lois that Leslie Larr is still in the wind, but they’re doing their best to find her. Once she’s in custody, the DoD will leave Smallville and things will get back to normal. He starts to apologize to Lois about the military side of what happened, telling her she’s proud of her for keeping her faith, which is what made the difference.
At a state of the art military prison, Edge is sitting in a green-K room, getting flashes of his father’s voice in his head.