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.

Clark meets Arthur "AC" Curry, a young man with extraordinary powers underwater. AC is in Smallville hoping to sabotage a Luthorcorp experiment that is threatening sea life. While in Smallville, AC forms an attraction to Lois.