Edward Teague is flying by charter plane to South America under a false ID when a stewardess approaches him: Kara. He doesn't know who she is but she asks him about Veritas. He denies knowing anything about it and Kara chokes him, demanding to know where the control orb is. Kara drives her fist through the side of the plane and threatens to throw him out, and he tells her that Lex Luthor might know. She flies out of the plane as it crashes to the earth.
Lex is at the Daily Planet when his bodyguard informs him that they've lost contact with two teams in the Arctic. Jimmy comes in to discuss his Kawatche article and Lex wants him to repay his favor of helping Chloe by getting Lois off of his back. He wants Jimmy to give her information about the Arctic location, and tells him to do whatever it takes, and threatens to turn Chloe over to the government if he doesn't.
Lois visits Clark and announces that there's an opening for an intern that he can fill. Clark isn't interested and she wonders why he was friends with Lex. Clark asks her to be careful working for Lex as Chloe arrives, and Lois takes off. Chloe knows about the crash and that Edward Teague's corpse has been identified. They go to Isis where Chloe has penetrated the government files and plays a sound recording from just before the crash. Clark uses his super hearing to identify Kara's voice and Teague telling her about Lex, but refuses to believe she could have caused the crash.
Kara arrives at Lex's manor and uses her x-ray vision to find the control orb hidden in a vault. She tries to touch it but it repels her. Clark arrives and asks Kara what she's doing, but she says she's trying to protect him and Teague brought it upon herself. He takes her to the barn to express his concerns and wonder if she's touched red kryptonite. She denies everything and warns that Clark could become the most powerful weapon on Earth in the wrong hands. He tries to get her to stay but she kicks free and flies away, insisting she'll do whatever it takes to save Earth.
Jimmy meets Lois at Ace o'Clubs and lies that Lex's Arctic expeditions have been for oil. She wonders if he's lying but he manages to convince her otherwise and she thanks him.
Lex returns to his study to find Kara waiting for him. She demands to know the truth about Veritas, and says she and the Traveler are from the same planet. When he doesn't believe her, she demonstrates her powers and says it's his destiny to defeat the Traveler. She has to admit that only a human can use the orb and he gives her the indicated coordinates. She assures him that a Kryptonian can get someone there and she believes that the Traveler will now destroy humanity. Lex asks who the Traveler is, and understanding crosses his face.
Chloe arrives at the farm to find Clark contemplating the lead box of kryptonite. He wonders if he hasn't done enough as Kara claims, and needs Chloe to use the kryptonite.
Lex is packing away the control orb when his bodyguard brings Jimmy in. Jimmy tells him that he succeeded with Lois and Lex insists he provide regular reports. Jimmy refuses and Lex says he respects his integrity then leaves for the Arctic.
Chloe calls Kara and claims that Clark plans to destroy the Fortress, and then tries to use the green kryptonite on her. It has no effect and "Kara" reverts to Brainiac. He drives metal probes into her head but she glows with energy before collapsing unconscious, and he wonders what exactly she is.
Aboard his plane, Lex orders the pilot to depart without waiting for Kara. He doesn't believe he can trust her, and figures the control orb will protect him against whatever destroyed his teams.
Clark visits Chloe at the hospital and realizes she's been infected with the same virus as Lana. Meanwhile, a weakened Brainiac goes to a power transformer station and recharges himself. Clark arrives and knocks him away, having figured that Kara was Brainiac since Krypton. Brainiac claims he's done something worse then kill Kara, and says the only way Clark can save Lana and Chloe is to kill Brainiac. He doesn't believe Clark can take another life but Clark drives electrical cables into him, noting that he's a machine. Brainiac "dies," but warns that Clark's own end is near and there's nothing he can do to stop it. Clark is unaware that Kara is trapped in the Phantom Zone.
Clark confirms that Chloe is okay then goes to see Lana. A nurse informs him that Lana had a full recovery and checked out, and gives him a CD from her. He plays it and Lana says that the world needs him more and she's holding him back, and asks him not to come after her. Lois comes in and they embrace.
A concerned Jimmy brings Chloe home and admits that he never had to face the fact he might lose her. He says he doesn't want to be without her, and offers her an engagement ring from the hospital gift shop. However, they're interrupted when government agents break in and arrest Chloe.
Clark is at the barn where Jimmy finds him and gives him the news. Jimmy explains how Lex blackmailed him and turned Chloe in, and then went to the Arctic.
Lex enters the Fortress and prepares to use the control orb. Clark arrives and the two face off. Clark tries to explain but Lex believes Clark is conspiring to destroy the human race by hiding among them, and insists he was prepared for a greater destiny to stop Clark. Clark insists that Lex has to choose on his own, and Lex goes to a crystal console and inserts the orb. It glows with energy and Clark collapses. Lex holds him and apologizes for it ending this way, as the Fortress collapses around them and falls into the earth.