During a rave party in the underground cave discovered by the Indian descendant Kyla Willowbrook, the student Travis has a reckless attitude climbing a lamp tower and dies. Soon after, Pete is pierced by a parasite hiding the cave wall, thus becoming reckless and bold. Meanwhile, Lex Luthor hires the linguistic specialist Dr. Fredrick Walden to decipher the meaning of the paintings in the cave. Clark invites Lana to date on the next evening. Later, Clark goes with Chloe Sullivan to the cave, and she is also pierced, changing immediately her behavior. When Pete puts a piece of red kryptonite in the pocket of Clark, he once against becomes 'Dark Clark' or 'Red Clark' in which the trio makes lots of trouble in Smallville and hurts the feelings of Lana.

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.

As Clark and Lana get more romantically close to each other, the comatose Dr. Fredrick Walden recovers and repeats the sentence "the day is coming, and he will rule the world" many times. He believes that Clark Kent is a menace to mankind. He escapes from the mental institution using a strong power he has achieved and tries to eliminate Clark. Meanwhile, Dr. Helen Bryce returns to Smallville for her engagement party with Lex Luthor, and finds her office broke in and the blood sample of Clark Kent stolen. But who took the blood sample and her office files? Lionel or Lex? Clark is asked by Lex to be the best best man, and Martha and Jonathan Kent to replace his missing parents, as Clark begins hearing voices coming from his spaceship. Also, the evil Lionel Luthor continues playing mind games by trying to poison the relationship of Helen and Lex, as well as Chloe and Clark by offering her an intern job in Metropolis in exchange for her to investigate Clark. But unfortunately, Lionel overhears the revelations of Dr. Walden to Lex about Clark being an alien.