Baby Kal-El lands on earth and is found by the Kents. Kal-El is named Clark by Jonathan and Martha and tries to live a normal teenage life. This is somewhat of a challenge given his developing abilities. He becomes fast friends with Lex Luthor after saving Lex's life. Same plot used as the aired pilot except for some extension to certain scenes and Cynthia Ettinger portraying the role of Martha Kent before Annette O' Toole takes her place for the rest of the series.
As Lex helps Lana prepare for the re-opening of the Smallville theater, The Talon, as a coffee shop, a man from Lex's past, named Jude Royce, arrives in town and begins stalking Lex wanting to hold him in conjunction with a shooting death at Club Zero in Metropolis three years ago that Lex may have been responsible for. Meanwhile, Chloe looks into Clark's past as an adopted child while Martha and Jonathan try to thwart Chloe's moves.
After stealing an experimental flower laced with meteor-rock pollen from Dr. Steven Hamilton, the employee of the Luthor Corp, James Beales has a truck accident on the road and is rescued by Jonathan Kent. However, the flower releases its pollen on Jonathan's face, and he unleashes his innermost repressed desires first with Martha and his anger towards the Luthors. He enters in coma later. Then Lana becomes affected and tries to seduce Clark. Pete also becomes affected by the Nicodemus flower in the same way. While Clark helps Lex track down the source, Lex hides from Clark that Dr. Steven Hamilton is working for him, but they find the cure in an old book.
Along the dispute of an election of the president in Smallville High School, candidate Paul Chan is severely injured by a swarm of bees. Pete decides to promote Clark Kent as the substitute for the spot. When the other aspirant schoolmate, Felice Chandler, is also attacked by bees, Clark believes that last competitor, Sasha Woodman, who has the meteor-rock ability to control bees, is behind the attacks. Meanwhile, Lex Luthor is threatened by an opportunist and ambitious reporter from Metropolis, named Carrie Castle, over some dark secrets of his that she's investigating. Also, The Talon, the thematic coffee shop where Lana works, is completely empty, losing clients to the competition; with the threat of closing the doors, Clark turns to Lex to ask for help to keep it open for Lana's sake.