| ShortSummary | - Brainiac propositions Kara at the farm, but she refuses; Brainiac warns Kara, and Clark, that not working with him will cause people to get hurt. Jimmy and Lois work together to uncover the truth behind Patricia Swann's murder. Lex begins searching for the secret of Veritas with a key he found in Patricia's pendant. Kara attempts to teach Clark to fly, but he is more focused on finding Brainiac, who attacks Lana at the Isis Foundation. In order to save Lana's life, Kara agrees to help Brainiac. Lana is placed in a clinic, stuck in a catatonic state, while Clark and Chloe have no leads as to where Brainiac and Kara are.
- Chloe intercepts confidential information from Lex, but the Black Canary shows up and steals the information back for Lex. When Lex learns the Green Arrow was involved, he sends Black Canary after him. Black Canary attacks Oliver, believing him to be a terrorist, and in the process reveals his secret identity to Lois. Clark confronts the Canary, and convinces her of the truth. Oliver offers Black Canary a spot on his team and she accepts, while Clark and Lana try to reconcile their relationship.
- Lana is unaware that Bizarro is impersonating Clark, who is still frozen at the Fortress of Solitude, and reveals information about Milton Fine to him. Bizarro tracks down Fine in the hope that he will help him combat his yellow sun weakness. Fine directs Bizarro to Dax-Ur, a Kryptonian scientist who came to Earth years earlier. Jor-El releases Clark from his imprisonment so he can defeat Bizarro. Clark receives blue kryptonite from Dax-Ur and uses it to destroy Bizarro. Clark unwittingly leads Fine to Dax-Ur, who uses Dax-Ur to restore his powers. After Grant reveals his true identity to Lionel, Lex has him killed.
- Lionel hires a group of men to kidnap Clark, using kryptonite tazers to subdue him, and lock him in a kryptonite-lined cell. Patricia Swann , Dr. Virgil Swann's daughter, comes looking for the "Last Son of Krypton" and accuses Lionel of taking the "Last Son" for himself, and having a hand in the deaths of her father, the Teagues and the Queens – three families who came together with Lionel, under a secret societal name of "Veritas", to welcome the "Last Son" to Earth. Chloe and Lana discover Lionel's actions, so they take Kara to Jor-El, who restores her memory; with her powers returned, Kara saves Clark. Patricia Swann gives Clark her father's journal; later, Lex has Patricia killed and a pendant she was wearing—which depicted the Veritas symbol—delivered to him.
- Clark and Lana team up to take down Lex, and discover, through an Isis Foundation patient, that Milton Fine is still alive. Adrian, one of Lex's experimental patients, plants a bomb on Chloe, threatening to kill her if Lois does not get Lex to admit that he is cloning humans. Lois confronts Lex, and, after Lois is knocked unconscious by Lex, it's revealed that the patient is a failed clone of Lex's brother Julian. Adrian also reveals that "Grant Gabriel" is the successful clone. Chloe, fearing that she will die, confesses to Jimmy that she was infected by the meteor rocks. In the end, it is revealed that Bizarro has been posing as Clark the entire time, unknown to anyone else, with Clark trapped at the Fortress of Solitude.
- Lois discovers that Lex has found Kara, who is suffering from amnesia, and follows him to Detroit after her. The busboy at the diner that Kara works is obsessed with her, and when Lex arrives, the busboy shoots him, fearing that he will take Kara away. He then holds Kara and Lois hostage. Clark, in efforts to find them, enters Lex's mind using experimental LuthorCorp technology; here he discovers Lex's good side, child Alexander, is still alive. Chloe uses her powers to bring Lex back from the dead, leading to a personal struggle with the moral aspect of her powers.
- Clark learns that Kara is in Washington looking for the crystal from her ship. Kara learns the exact location of the crystal, but it is not there when she arrives. Clark confronts her in a club, but she flies away. With Jimmy's help, Kara follows a path to Lex's mansion, but Agent Carter is waiting. Using kryptonite handcuffs, Carter takes Kara back to Virginia. Using a kryptonite truth serum, Carter attempts to learn about Krypton, but Clark interrupts him and saves Kara with Lionel's help. Clark shows Lana that he has Kara's crystal, which contains his birth mother's DNA.
- Clark uses Kara's crystal to resurrect his mother Lara, but unknowingly brings Zor-El back. Lara unwittingly gives Clark a blue kryptonite ring that strips his powers, while Zor-El tries to take over the world. Lois and Grant's romantic relationship is discovered by Lex and Chloe. Grant and Lex are revealed to be working together, and Grant is revealed to be Lex's younger brother Julian Luthor. Clark gets to the Fortress and shatters the crystal, which destroys Zor-El and Lara. Kara is transported to Detroit, with no memory of who she is, and Jor-El informs Clark there will be consequences for his repeated defiance.
- Lex takes Lionel's locket, which holds the second key to the deposit box in Zürich, and then throws him out the LuthorCorp window to his death. Lex soon discovers the key is not where he thought, and heads to the Daily Planet to find it; he also begins having hallucinations of his younger self. Lex finds the key in Chloe's desk, and then fires her. Jimmy and Lois discover that Lionel was murdered. Clark confronts Lex at the mansion, informing him that he has proof Lex murdered Lionel. Lex's assistant destroys the evidence, and discovers Clark's secret. Before she can tell Lex everything, a mysterious stranger kills her.
- Lightning strikes a windmill on the Kent farm while Clark is weakened by nearby kryptonite; the bolt travels through him and Lana, transferring a portion of his powers to her. After sharing their first intimate moment in two years, Clark begins to worry about Lana's use of the powers after remembering what happened to Eric Summers and Jonathan Kent when they were imbued with Clark's powers. Lana becomes more aggressive with the powers, stealing confidential files from Lex—which show that Lex has been keeping what remains of Milton Fine's ship—and later attacking him. After a battle with Clark, Lana's powers are reabsorbed when Clark uses a high voltage shock and kryptonite to take the powers back; during the fight, Fine's remains are released.
- In order to locate Brainiac and Kara, Clark has Chloe hack into government satellites. The Department of Domestic Security has been monitoring Chloe's activity and, convinced she is a terrorist, convince Jimmy to work with them to bring her down. Clark decides to head to the Fortress to find a way to save Lana, where he learns that Kara is at Krypton trying to warn Clark that Brainiac intends to kill the infant version of Kal-El. The Feds have Jimmy accompany Chloe to a club, which is a front for a security building, to find out who her target is. The Feds catch Chloe stealing satellite images and begin interrogating her. Jimmy shows up and saves her life, and agrees to do whatever Lex wants in exchange for clearing Chloe's name with the government.
- Jor-El sends Clark to an alternate reality to show him what the world would be like if he never arrived on Earth. Here, the Kents have a natural-born son, Chloe is engaged, Lana married a french philanthropist, Lois is a Pulitzer Prize–winning journalist, Kara is the head of the Department of Domestic Security using the alias Linda Danvers, and Lex is the President of the United States. In this reality, Clark is unable to prevent Brainiac and Lex from detonating the country's nuclear missiles. After learning the world needs him, Clark is sent to Krypton to prevent Brainiac from killing him as an infant. After stopping Brainiac, Clark and Kara both return to present day Earth.
- While filming takes place on the Warrior Angel movie on the Kent farm, Clark saves lead actress Rachel Davenport from a car crash. After some researching by Chloe, it is discovered that someone is trying to kill Rachel, because they believe her character should die, like she does in the comics. Clark's secret is uncovered by the attacker when he is witnessed stopping a bullet intended for Rachel; he attempts to kill Lana in hopes that her death will make Clark see his true destiny as Earth's savior. Lana is revealed to be the one who kidnapped Lionel Luthor, and when he is finally freed, Lionel informs Lana that he knows she kidnapped him.
- The bank teller from Zurich attacks Lex, carving the Kryptonian symbols for "Traveler", "Savior", and "Sanctuary" into his chest. After seeing the symbols, Clark travels to Montreal, Quebec, where he finds Edward Teague , Jason Teague's father, the only surviving member of Veritas. Edward deems that Clark is no savior and attempts to kill him so that Lex cannot control him. Chloe saves Clark, who in turn saves Edward from Lex, who arrived looking for more clues to controlling the Traveler. Lex returns home and discovers an orb hidden inside the mantle above the fireplace. The orb gives the location of the Fortress of Solitude.
- Kara informs Lex that he will defeat the Traveler, who is really destined to destroy mankind, and sends him to the Fortress of Solitude. Clark learns that Brainiac has been impersonating Kara, who is actually stuck in the Phantom Zone, and destroys him to finally free Lana from her comatose state. Lana leaves Clark a DVD stating that she is holding Clark back, and the only way for him to help the world is if the two of them are not together. The DDS arrest Chloe just as Jimmy is about to propose marriage; Jimmy goes to Clark and tells him about the deal he made with Lex, also informing him that Lex is headed to the Arctic. Clark arrives at the Fortress just as Lex, who now knows Clark's secret, places the orb onto the crystal control panel, bringing the Fortress down around him and Clark.
- Kara decides she wants to join the Miss Sweet Corn Pageant. Clark tries to teach Kara to control her abilities, so she does not expose their secrets, but gets frustrated with her lack of concentration. Lana returns to Smallville, with all legal charges dropped against her, and reunites with Clark. Tyler and Tempest, two meteor-infected pageant contestants who witness Kara using her abilities, convince Kara to help them steal some buried treasure. The treasure turns out to be an SOS alert from another Kryptonian on Earth. Lex confronts Kara and promises to find out the truth of her abilities.
- Pete Ross chews some kryptonite-laced gum and develops the ability to stretch his body to extreme lengths, which he uses to save Kara's life from a falling speaker at a OneRepublic concert in an abandoned warehouse. Pete arrives at the Kent farm and gets up to speed on who knows Clark's secret, before revealing his own power to Clark. Pete decides to reveal his ability to the world, against Clark and Chloe's advice, but Lex blackmails him into stealing Kara's bracelet from Lionel's safe. When Pete does not deliver, Lex tortures him; Clark arrives and saves Pete. Kara, no longer trusting Clark and Lana, stays with Lex, while Clark secretly hides the bracelet.
- Chloe learns that Dr. Curtis Knox has a surgical cure for those affected by kryptonite, so she sets up an appointment, knowing a side effect could be memory loss. Knox turns out to be an immortal serial killer, and also turns out to be Jack the Ripper. John Jones shows up at the Kent home and warns Clark that he cannot trust Kara. John explains that her father, Zor-El, attempted to assassinate Clark's father. Clark is told to find Kara's crystal before she does, but he is side-tracked fighting Knox, who is attempting to take Chloe's heart and transplant it into the woman he loves. Lana uses the $10 million she stole from Lex to buy surveillance equipment to spy on him.
- Clark discovers he has a cousin, Kara, who was stuck in suspended animation for eighteen years. After a rocky first meeting, where Clark and Kara fight, the two soon band together to find Kara's stolen ship. Together they find her ship, which was taken by the Department of Domestic Security, but it is in self-destruct mode. Kara absorbs the explosion before it can kill anyone. Later, Kara reveals that a Kryptonian crystal, hidden inside the ship, was stolen before the ship exploded. Lex finds Lana, who used a LuthorCorp clone of herself to help fake her own death, in China. Lex returns to Smallville, determined to find the girl—Kara—who saved his life.
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