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.

Clark gets an inverse make-over from Lois, in order to become a gray mouse when the Blur goes public. Just then, a flashy media-hungry new superhero emerges: Booster Gold, who systematically steals the show. Clark discovers Booster came from the future with a Legionnaire's ring, probably stolen. Generally bullied, shy schoolboy Jaime Reyes is inadvertently infected with the alien scarab which Booster was hired to retrieve for industrialist Ted Kord, hence transformed into the Blue Beetle, an uncontrollable monster. Clark could just expose Booster as a fake coward, but chooses to educate him in superhero ethics.