Clark discovers that he has X-ray vision, but struggles to use it properly. Meanwhile, shape-shifter Tina Greer robs a bank impersonating Lex Luthor, and then decides that she wants to become Lana Lang - permanently.

Lana befriends Harry, an elderly murderer living incognito in a nursing home. He falls into a Meteor Rock pond and regains his youth. Harry starts killing descendants of the jurors who convicted him, one of whom was Jonathan Kent's father.

Earl Jenkins claims that his violent shaking disease was a result of illicit experiments on Level 3 of Luthorcorp. Lionel denies that it exists, so Earl takes a plant tour group hostage. Lex offers himself in exchange for the hostages.

Corrupt detective Sam Phelan learns about Clark's abilities, and he offers to keep quiet if Clark steals some internal police files. When Clark refuses, Phelan frames Jonathan for murder to extort Clark into stealing from Luther Corp.

Clark and classmate Eric Summer are both struck by lightning while Eric is holding a meteor rock, and Clark's powers are transferred to Eric. While Clark experiences normal humanity, the emotionally challenged Eric goes on a rampage.

As Lex helps Lana prepare for the re-opening of the Smallville theater, The Talon, as a coffee shop, a man from Lex's past, named Jude Royce, arrives in town and begins stalking Lex wanting to hold him in conjunction with a shooting death at Club Zero in Metropolis three years ago that Lex may have been responsible for. Meanwhile, Chloe looks into Clark's past as an adopted child while Martha and Jonathan try to thwart Chloe's moves.

Lana develops a form of clairvoyance after being injured by an explosion, and she has visions of the activity of a local serial kidnapper and killer. When Chloe is kidnapped, Clark must rely on clues from Lana's visions to save her.

Clark saves Lana from the tornado, leading Lana to be suspicious of Clark. While protecting Clark's secret, Jonathan gets trapped with reporter Roger Nixon in an underground mausoleum. Lex and Clark search for Jonathan.

When the "hot" new Biology teacher Desiree Atkins (Krista Allen) arrives in Smallville, Clark Kent gets excited in her presence and his hormonal surge sets off a new ability: heat vision. Lex Luthor meets and falls for Atkins and they decide to get married. Meanwhile, Clark's heat vision causes another fire at The Talon when Clark is talking with Lana, leading Clark to get briefly jailed on suspicions of arson. Lex invites Clark to be his best man, but when Desiree tries to seduce Clark, he realizes that she is a meteor freak with the power to seduce men.

Lana Lang finds some poems from a secret admirer in the gravestone of her parents in the cemetery. Later, she meets the author, Byron Moore, a weird teenager kept locked by his parents in the basement of their farmhouse. They believe the boy is abused by his parents, but soon they realize that he was the subject of an experiment of a laboratory of Luthor Corp, which made him powerfully evil and super-strong when he comes into contact with sunlight. Meanwhile, Martha Kent is invited to work as the assistant of Lionel Luthor, and she accepts the invitation under the reluctance of Jonathan Kent.

A woman appears in Smallville claiming that Clark is her biological son by Lionel Luthor, and she kidnaps Lex to force a confession from Lionel. Clark demands that his parents explain what role Lionel Luthor played in his adoption.

Clark rescues mind-reading Ryan James from a research hospital that treats him like a lab rat. Ryan's guardian doctor sues to get Ryan back, and Clark learns that Ryan has a brain tumor that needs treatment.

While practicing motocross with Pete, Clark Kent falls down through a hole in an underground cave and meets a young Native American woman named Kyla Willowbrook (Tamara Fieldman). Kyla is investigating some mysterious ancient paintings in the walls of the cave, and she and Clark immediately fall in love with each other. Her grandfather Professor Willowbrook and some ecologists are fighting against the construction of a Luther Corp building that will destroy the caves, but generate 1,000 new jobs in Smallville. Martha becomes split between the both interests, but the blind Lionel is motivated only by greed and self-interest to keep the project open, while Lana rallies the rest of the town in a protest to stop the construction project. Meanwhile, a mysterious wolf-creature kills a construction foreman, and threatens Martha and the blind Lionel. Following investigation by Chloe, Clark believes that the Professor Willowbrook is a mutant with the power of transforming himself in a wolf. But the real culprit is Kyla.

Lionel Luthor is shot twice in the Luthor's mansion by an unknown assailant. When Jonathan Kent is found drunk, with a pistol in one hand and a bottle of tequila in the other hand sleeping in his truck, he becomes the prime suspect of the attempt. All the evidences point to him, but Clark believes in his innocence and tries to prove that his father did not shoot Lionel. Clark and Pete team up to investigate leads Lionel had, and learns that the conspiracy to frame Jonathan goes back to the town sheriff. Meanwhile, Lex deals with his father's associate, Dominic Senatori, who thinks Lex was the culprit who shot Lionel, but Lex thinks Dominic is the guilty one. Meanwhile, Lana asks Chloe to investigate Henry Small after he refuses to take Jonathan's case.