Edward Teague is on a private jet when the flight attendant approaches him. It is Kara Kent beginning to question him about Veritas and a device. He avoids her questions and she grabs him by the neck and punches a hole in the side of the plane. She threatens to throw him out, until he admits that Lex Luthor probably has the information she seeks. Kara flies out of the plane, destroying the tail and causing it to crash.
Lex is in his Daily Planet office when he is informed that two of his teams have gone missing trying to reach their target in the Arctic Circle. Jimmy Olsen enters and thinks he is meeting Lex about his upcoming Kawatche Caves article. However, Lex reminds him that he did Jimmy a favor by calling the Department of Domestic Security and keeping Chloe Sullivan out of prison so he wants Jimmy to distract Lois Lane, who has been asking too many questions about him. Jimmy is reluctant because Lois is quite persistent but Lex has forced his hand. He gives him bogus satellite images to throw Lois off the trail.
Clark Kent answers his door to find Lois eager to see him. She explains that since Chloe was fired, a spot has opened up in the bullpen. She gives him an application and says she thinks he is destined for greater things than working on a farm. Clark points out that he'd never work for Lex and Lois asks why they were ever such great friends. Clark just says that sometimes people don't turn out the way you think they will. He warns Lois to be careful working for Lex. Chloe arrives and asks to talk to Clark in private. Lois exits and Chloe tells Clark that Teague has just died in a plane crash.
Clark and Chloe go to the Isis Foundation where she explains that she has hacked into the plane's black box and learned details about the crash. She plays garbled audio and Clark uses his super hearing and is surprised to hear Kara's voice, threatening to bring the plane down. They wonder if Kara is as dangerous as other Kryptonians they have come in contact with but Clark is reluctant to believe that Kara is a killer. Chloe plays more audio and Clark hears that she's going after Lex.
Kara arrives in the Luthor Mansion and uses her X-ray vision to locate the orb in Lex's safe. However, there is a fail-safe protection within the orb, preventing anyone other than a human from using the device, which means she is unable to take it for herself. Clark finds Kara and asks her about the plane crash. Kara says she was only trying to protect him and killed Teague for going after Clark. He grabs her and speeds her back to the barn. He questions her strange behavior, suggesting she has come into contact with red kryptonite or has changed on returning from the past. Kara insists that she is fine. She tells Clark that if someone figured out how to control him, a lot more innocent people might die, and that she is going to do whatever it takes to save Earth. She flies away and when Clark tries to hold her back, she kicks him across the barn and departs.
Jimmy meets Lois at the Ace of Clubs and gives her the satellite images. He convinces her that Lex has been visiting the Arctic looking for new places to drill oil. Lois is skeptical but Jimmy says he got the photos from the photo lab and Lois seems convinced.
Lex finds Kara in his library, and she begins to ask him questions about Veritas. She tells him that she wants the device that can control the Traveler. She says she and the Traveler are from the same planet and demonstrates for Lex by using her heat vision. Lex realizes that Kara is in fact the being that saved him at Reeves Dam. Kara tells him that she saved him because it is his destiny to defeat the Traveler. She says the device is designed so that only a human can use it. She tells him to take the device to the co-ordinates in the Arctic and that she will help him find it. Lex doesn't understand why Kara would help destroy one of her own kind but Kara claims that she knows the Traveler's true destiny: to destroy mankind. Lex asks who the Traveler is, and Kara suggests that he already knows.
Chloe finds Clark at home with the lead box. He tells her that kryptonite is the only way to stop Kara. He is worried that Kara is right: that he hasn't done all he could to stop Veritas. He asks Chloe to help stop Kara but Chloe points out that the green kryptonite will incapacitate him as well, and that she should do it alone.
Lex is preparing to take the device to the Arctic and tells his men that another passenger is coming. Jimmy arrives and tells him that he did what Lex asked and gave Lois the photos. He thinks they're even now but Lex tells him to continue to spy on Lois. Jimmy objects, saying he doesn't want to lie anymore. He promises not to tell anyone about Lex's secrets and is pleased with himself when Lex seems to agree.
Chloe lures Kara to her apartment, but is shocked when the green K doesn't work. Kara realizes that Chloe has deceived her, prompting Chloe to try and escape the apartment. Kara blocks the door and reveals that 'she' is actually Brainiac impersonating Kara. Changing back into Milton Fine, he tells Chloe he is impressed that she tried to stop him, but tries to pierce her head with his finger tendrils. However, Chloe's power enables her to resist him and by the time she falls to the ground, Brainiac is considerably weakened and unable to continue his attack. Lex boards his jet and decides not to wait for Kara, being uncertain if he can trust her. The security team is reluctant to leave, since his last two teams have disappeared, but Lex is convinced that the device will protect him.
Clark goes to see Chloe in the hospital. He sits by her side and apologizes. Suddenly her eyes open; they are clouded over, and Clark realizes that she has been attacked by Brainiac. Brainiac is out seeking high voltage lines to recharge himself when Clark arrives and apprehends him. Clark now realizes that the real Kara never came back from Krypton, with Brainiac admitting that he was already impersonating her, having overcome Kara when they were out of Clark's sight. When Clark asks if he killed Kara, Brainiac says it is much worse than that. In a rage, Clark attacks him and demands that he release Chloe and Lana Lang. Brainiac points out that Clark would never kill him, as he needs to do to release them, because it is against his nature. But, in a defining moment, Clark retorts that Brainiac is not a man, but a machine, and using the nearby power supplies, electrocutes him until he explodes.
Kara is now seen trapped in the Phantom Zone, with the young Kryptonian spinning through space in one of the Phantom 'prison discs'.
Clark confirms that Chloe is okay as he goes to visit Lana. However, he is shocked to find her room in the hospital empty. The nurse explains that she made a sudden and miraculous recovery and checked out and has left Clark a DVD. Back at the farm, Clark watches the video, in which Lana explains that she felt unable to tell him in person. She says they were fooling themselves by thinking they were meant to be together. She says the world needs him more than she does. She tells him she loves him more than he will ever know, but asks Clark not to look for her. Lois arrives just as the video is ending. Clark starts to cry and she gives him a hug.
Jimmy is bringing Chloe home from the hospital. He is very nervous and admits that when Chloe was in the hospital he realized how much she means to him. He gives her a plastic ring and proposes. Before she can answer, armed agents from the Department of Domestic Security storm into the Talon and place Chloe under arrest. Jimmy tries to protest, but they punch him to the ground. As they are hauling her off, Chloe screams for Jimmy to call Clark. Jimmy finds Clark in his loft and tells him Chloe got arrested. Jimmy admits that he made a deal with Lex, but backed out of it, and says that Lex is now headed to the Arctic Circle.
Lex is in the Fortress of Solitude and is about to place the orb into the glowing console. Clark makes it to the Fortress where Lex is waiting. They stare each other down. The orb glows in Lex's hand. Lex says that Clark has brilliantly been disguising himself as a mild-mannered farm boy, but is secretly plotting mankind's demise. Clark protests, saying he's never hurt Lex. Lex counters that Clark never trusted him, and that they could have worked together to enable Clark to become a hero. Clark says Lex has no right to control his life, but Lex believes that it is his birthright to save mankind. He believes that all of his suffering has led him to this point. Then, saying "You'll never threaten the world again - Kal-El", Lex places the orb into the console where it glows brightly and precipitates the breaking apart of the Fortress. Clark falls to the ground, and Lex kneels down and holds him and tells him that he'd loved him like a brother. The Fortress collapses around them.