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.

Clark has some weird dreams with the cave and about flying. When he puts the octagonal key in a hole in the wall of the cave, he immediately learns how to decode the symbols. Then, while waiting for Chloe at the Kents' farm, his uncontrolled vision burns a symbol on the wall of the barn. Chloe publishes the picture in the front page of The Torch, and Clark soon receives an e-mail from a wealthy and prominent scientist from New York. Clark goes to New York and meets the reclusive and quadriplegic Dr. Virgil Swann, who tells Clark about his origins from the planet Krypton, his real birth name of Kal-El. Clark also finds another message in the spaceship which troubles Clark. Elsewhere, Dr. Waldon finds the octagonal key left behind in the cave and when he puts it in the cave hole, he gets hit with the so-called Kryptonian knowledge which overloads his brain and ends up in coma, which further fuels Lex's suspicions about the cave and Clark. Also, Lana considers moving out of Chloe's house to look for a place of her own.

After Lex discovers that Chloe's mother, Moira, has the power to control meteor freaks, he develops a drug to wake her from her catatonic state in the asylum, then he threatens to kill Chloe unless she uses her power to help him recover several meteor-freak escapees from his lab '33.1'. Clark helps Chloe break into the asylum to rescue Moira and finally get to know her mother, and he is almost tempted to kill Lex, but lets him live... again. Meanwhile, Clark rescues Lana from one of Lex's 33.1 escapees, and she later discovers something shocking about her "pregnancy." Also, Chloe decides to write an article about Lex's 'Project 33.1', but Lex silences her by threatening to have her locked away unless she remains quiet about his secrets projects.