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.

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.

When Lex Luthor loses a $150 million contract to Luthor Corp, he finds that his mansion was bugged by his father. He hires a team to bug the offices of Luthor Corp expecting to find the building empty since it is Sunday, but Lionel Luthor assigns Martha for work in his office with him. Jonathan becomes very upset, since it is their wedding anniversary, and he was planning a picnic with Martha. Lex calls off the action, but the leader of the group of industrial spies is killed by a member who wants to steal the contents of Lionel's safe. Martha and Lionel become hostages of the criminals, and when they open the safe, a great secret is disclosed. Meanwhile, Lana schedules a meeting with Mr. & Mrs. Small in The Talon to get to know Jennifer Small, who warns Lana about her husband.

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.

When a van of Luthor Corp is hijacked by three criminals, Clark accidentally witnesses the robbery. He recognizes the leader of the gang, Eric Marsh, a baseball player of Smallville high school. Unwilling to report his suspicious to the pompous Sheriff Adams, who continues intimidating and harassing the Kents, Clark launches his own investigation and discovers that Marsh and his two friends are using refined kryptonite to use as inhalers to give them super-human strength. Meanwhile, Clark quits his job at school paper, The Torch, after discussing with Chloe about him missing a few too many deadlines. Lana sees Jennifer Small with her lawyer, and she tells Lana that she plans to divorce Henry Small. Also, Lex tries to find what cargo was stolen from his father by trying to follow Eric Marsh, while Lionel arrives in Smallville for a surprise visit to Lex, and to Chloe whom he offers her a job as an intern at the Daily Planet newspaper in Metropolis.