Clark arrives home in the morning and finds Tess in his kitchen with a cup of coffee. She claims she just wants to catch up, and an awkward conversation ensues. Tess finally tells him that there's a problem with Alexander, and he needs Clark to guide him. Clark doesn't understand why, until Tess explains that Alexander is going through a metamorphosis. They hear a crashing noise and go to investigate, and find Alexander hefting a tractor above his head with his bare hands. Tess whispers to Clark that half of Alexander's DNA came from Clark.
Later, Lionel goes to the ruins of one of the Cadmus facilities and finds Tess waiting for him. He explains that one of his accountants located the facility, and he's there to find Alexander. She warns him that in this world, Lex killed his father, but Lionel just believes that shows that Lex was a true Luthor. He admits that he made a mistake in the other world when he chose Clark over Lex, but Tess him that the Luthor line will end with him. As Tess goes, Lionel tells her that he would have given her up for adoption just like his counterpart did, because she's inferior. He insists that Alexander could do great things with the proper guidance, and Tess admits that he's right. She leads him to a hidden chamber and shows him a container holding what she claims is Alexander's ashes after he died of the accelerated mitosis. Lionel doesn't believe her, but Tess invites him to check the bones for DNA and verify her claim.
Clark has Alexander doing chores at the barn, and he admits that it's better than being studied in a lab. He's taken the name "Conner," based on the name of the project that birthed him, Cognitional Neuralplastic Replicant, or CNR. Clark assures the boy that Tess is just trying to protect him, and that people often come to accept freaks. Conner explains that he can't remember anything due to his "mutation," and he wants to find out why he's the way he is. When he tries to leave at superspeed, Clark blocks him and Conner realizes that they have the same powers, and that Clark is the Blur. He wants to go to Metropolis to save people, but Clark says that he needs practice. Lois comes in and Conner is struck dumb. His eyes glow red and his heat vision goes out of control, and Clark redirects it just in time.
Clark gets Lois alone and explains what is happening, including the fact that Conner has some of his DNA. Lois believes that Conner is still a risk, but Clark says that he can understand what it's like to feel like a freak, and tells her that the feeling never goes away. The only thing that has made him feel normal is her. Lois tells him that Conner because he has the two of them.
At the Planet
, Lois is photocopying books on raising teenagers when Tess comes in and says that they have to deal with Conner once and for all. She warns Lois that if Lionel gets hold of Conner, he'll use him to conquer the world just like he did on the other Earth. Lois says that they have a choice and suggests that they try to find a detail that Lionel overlooked when he took over his dead counterpart's identity.
Lionel has his hired scientists confirm that the remains came from a clone. The scientist tells him that they learned from Dr. Lamell that Conner is in Smallville and Lionel goes to get him.
Conner is in the barn practicing with his heat vision when Clark arrives and explains that they have to take responsibility and learn control. The boy tries again and burns Clark's clothing. Clark returns to the house and finds Tess there. She notes that Clark is feeling proud of Conner, and then warns that her man on the inside has told her that Lionel has found Conner. They discuss that half of Conner's DNA is Lex's, unaware that he can hear them with his superhearing. He superspeeds away.
Lois breaks into Lionel’s office and takes photos of all of his papers. She calls Tess to tell her she's had no luck yet and then signs off... just as a guard captures her.
Conner goes to the fire-gutted shell of the Luthor manor and finds a photo of Lionel. Lionel comes in and Conner asks why he is there. The Luthor patriarch says he's there to answer his questions and tries to approach him. Conner keeps his distance, and Lionel tells him that a part of him is Clark Kent. When Conner reveals that he knows he has some of Lex's DNA, Lionel claims that Clark is afraid of him and wants to keep him away from the empire that Lex created. He gives Conner a box with a ring of red kryptonite, and claims that it's the Luthor birthright. When Conner dons it, the red kryptonite takes effect.
Lionel takes Conner to the slaughterhouse where he's holding Lois. When he claims that Clark sent his fiancé to investigate him, Lois says that she came on her own. Lionel says that he'll kill to keep Conner with him, and draws a gun. Lois doesn't believe he'll shoot, since the one she knew would never get blood on his hands. Lionel says that he's not the Lionel she knew and prepares to shoot, but Conner whisks her away to the street. When she says that she's cold, he gets her a fur coat and then steals some jewelry. Lois realizes that he's affected by red kryptonite, and Conner steals a car so they can make their escape.
At his office, Lionel checks in with his people and tells them to make sure that Conner keeps the ring on because it has a tracking device, and that Lois can't lead the boy to Clark. Clark enters the office and shows him the red kryptonite ring that he found. Lionel insists that the red kryptonite unleashes the dark side of its wearer, and he wants to see Conner's dark side. Clark says that he won't let Lionel harm Conner like he did Lex, but Lionel notes that Clark hid the truth and betrayed Lex, and did the same to Conner. He says that as Conner becomes increasingly unstable, he'll take away everything Clark holds dear, including Lois.
Conner takes Lois to the manor ruins and promises to keep her safe. She tells him that she's with Clark, and Conner throws her into a wall and knocks her out. Lois wakes up and finds that Conner has started a fire and lit candles. He apologizes for striking her, and Lois suggests he get some champagne. Conner easily realizes that she's lying and insists that he's at the top of his game thanks to Clark. Lois warns that the red kryptonite is bring out the Lex side of Conner's genetics, but Conner throws her to the floor and says that he'll kill her to keep her from Clark. Clark arrives and Lois stumbles away, while Conner tells him that he's not welcome there. When Clark tries to warn the boy, Conner attacks him and sends him flying. Clark rallies and says that Conner isn't acting like he really is, but Conner knocks him away again and says that he's a Luthor. Clark says that he's coming home with him and slams him into the wall, and then smashes the ring.
As Conner recovers, both of them collapse in pain as Lionel arrives with a piece of kryptonite. He knocks Clark to the ground, leaves the kryptonite next to him, and then hauls Conner out of range of the radiation. Conner stares at the dying Clark and then uses his heat vision to destroy the kryptonite. Lionel slips away as Clark recovers and assures Conner there's nowhere for their nemesis to hide.
Later, Lionel is at his LuthorCorp office, drinking scotch, when Tess comes in and tells him that security is on their way to escort him out. Lionel is unimpressed until Tess explains that she found one document that Lionel didn't know about: her orphanage papers. The fingerprints on them are from the mirror Lionel and are in reverse, meaning she can prove he's a fake. Tess tells him to relinquish control of LuthorCorp. When he wonders why, she tells him that she laced his drink with nano-tracers and can follow him anywhere. Tess warns that if he tries to strike at her friends, she'll have him killed. When Lionel wonders why she doesn't finish him off now, Tess says that's not who she is. As Lionel is escorted out, he warns Tess that she'll always be a Luthor.
Conner is performing chores to make up for the trouble he caused, and Clark apologizes for lying to him. The boy admits that he's not the same as Clark because of his dark side, but Clark assures him that he'll make the right choice. Conner suggests he should start dressing the part and reveals that he's made his own version of the Blur costume. Clark shows him an application for Smallville High, made out to Conner Kent. As Conner leaves to fixes the fence, Lois arrives and admits that Clark was right for nurturing Conner. She apologizes for investigating Lionel without telling him, and Clark admits he has a new respect for his mom and dad for raising him properly and handling the responsibility. Lois says that when they have kids of their own, she's sure he'll be an amazing father.
At Lex's grave, Lionel mourns the loss of his son for depriving him of rulership of the world. He says that he'd give anything to have Lex at his side... and Darkseid appears before him.