Lex returns to Smalville and the Lex mansion, and invites Dr. Helen Bryce for a second honeymoon while trying to find out if it was her or his father who attempted to kill him. Meanwhile, Clark also returns to Smallville and the Kent farm, but Morgan Edge finds him and threatens to kill Jonathan and Martha in to get what Clark stole from Lionel Luthor's safe, which is the stolen vial of Clark Kent's blood. With the financial status of the Kent family in dire straights, the farm is sold in an auction, but there is a surprise in the end. Also, Lana tries to declare her love for Clark, but he rejects her love out of fear that she may discover his secret. Clark also returns to Smallville High and to the Torch newspaper under Chloe who continues to investigate Clark's origins.

Gabriel Duncan is a deranged teenager who breaks in the control room of a nuclear silo in Smallville, kills the two security guards, and starts the launch sequence to send one missile to destroy Smallville in one hour. He calls his friend Chloe, who is moving to the university, and asks her to leave the town that he wants to destroy because of the population of "meteor freaks." The army does not know which of the sixteen silos might have been broken in by Gabriel. Meanwhile, Clark and Lana sleep together in his room and early in the morning, Lana sneaks out of the house, but Jonathan and Martha see them. When Chloe calls Clark, he plots a simulation of a car accident with Chloe to force Gabriel to disclose his position. When Gabriel meets Chloe, Clark is deadly shot by the insane teenager, dying in the hospital. Suddenly, Lionel Luthor awakes from his catatonic situation in Belle Reve and Clark's body vanishes from the hospital which leads to both meeting at the Kryptonian Fortress of Solitude at the North Pole which leads to a surprising discovery for Clark. Elsewhere, the evil Lex continues to obsessively study the black spaceship at the LutherCorp warehouse and discovers that something else has climbed out of the ship.