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.

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.

Lex and Lionel engage in a struggle over closing down the fertilizer plant. Reporter Roger Nixon steals Clark's spacecraft and learns his secret. Whitney joins the Marines, and Clark takes Chloe to the prom, while a huge tornado approaches.

Ian Randall is a mentally unbalanced, overachieving student desperate to succeed who gets a 'C' from his stern shop teacher John Frankle. Ian freaks out, duplicates himself and kills Mr. Frankle. The meteor-rock mutant simultaneously invites Lana and Chloe on a literal 'double date', aiming to get a scholarship from Luthor Corp to Yale by using the girls who know Lex Luther. Meanwhile, Lana moves to Chloe's house to live with her and divorced father after Nell leaves town. Clark tries to advise Lana and Chloe about the personality and ability of Ian, but he is misunderstood. Elsewhere, Jonathan breaks his leg, and Lex Luthor meets Dr. Helen Bryce, who is treating Jonathan where an immediate attraction develops between Lex and Dr. Bryce.

At the Kent farm, Clark Kent is surprised in the middle of the night by a naked young woman claiming that she is Kara from Krypton, and asking him to go with her somewhere through the Kawatche caves to be "re-born" with the spirit of Jor-El. Kara also forces Jonathan to reveal the secret deal he made with Jor-El at the beginning of the season. Meanwhile, Clark decides to testify against Lionel to keep him in prison. Lionel sends a key of the secret chamber in the Luthor Mansion to Clark where he finally discovers the reason for the last three years of Lex's personal investigation of him, and he ends his friendship with Lex. Agent Loder continues investigating Clark's origins, until Kara finds him eavesdropping on the Kents and she eliminates Loder for good. Also, Lana leaves for Paris and Chloe and her father are included in the witness protection program. Events come full circle as Jonathan unsuccessfully tries to stop Clark from traveling through a dimensional gateway in the cave wall, Martha observes a Kryoptonia symbol that appears in a open field, Lex is alone in the mansion when he had a drink of brandy which is poisoned, Chloe and her father arrive at a FBI safe house... which explodes with them still inside, and Lionel accepts his new look in prison, but satisfied knowing that his revenge against all those involved with his incarceration has been accomplished.

The mystery surrounding Chloe's death deepens as Clark and Lois investigate, discovering that Lex Luthor and Lois' abrasive and militarist father, U.S. Army General Sam Lane, are somehow involved. Meanwhile, Lana returns to Smallville after finding out that the symbol that appeared on her back in Paris is also on the cave wall. In prison, Lionel Luthor prepares for his murder trial and sends out a liquid-metal assassin to keep Clark and Lois from investigating Chloe's 'death'.