Under the influence of red kryptonite, and living in Metropolis, Clark gets involved with a crime lord named Morgan Edge who hires him to break into LuthorCorp. Desperate to put his family back together, Jonathan makes a deal with Jor-El so that he can bring Clark home. Lex is stranded on a deserted island, with the world believing him to be dead. At the mansion, Lionel accuses Helen, revealed to be alive, of killing Lex.

Jor-El grants Jonathan temporary superpowers, and he and Clark engage in a destructive battle below the LuthorCorp building. Clark, unable to kill his father, destroys the red kryptonite. Lex returns home to the shock of Helen. He quickly learns that Helen attempted to kill him and takes measures to ensure that doesn't happen again. Morgan Edge finds Clark and kidnaps him in an effort to make amends to Lionel.

Clark discovers his abilities are derived from the Sun, when an increase in solar flares cause his powers to either flare up, or give out completely. Perry White, a once promising journalist, arrives in Smallville in search of stories for a tabloid news show. Despite being constantly inebriated, Perry believes he witnessed Clark using superhuman abilities, and devises a dangerous scheme to expose the truth.

Lex locates Morgan Edge who underwent plastic surgery and gets him to admit that he helped Lionel murder his parents. Before Lex can take it to the authorities, someone tries to kill him. Lex flees and asks Clark for help. Evidence begins to amount that suggests Lex has had a psychotic break. Lex watches Clark slam into Edge's car, after Clark pushes him out of harm's way. Lex's doctors arrive and take him to Belle Reve sanitarium.

Clark discovers that his schoolmate Jordan can foresee the future, and he is horrified when Jordan predicts that Lana will die in a fire in the next few days. Meanwhile, suspicious of Adam's behaviour, Chloe investigates his background and finds some disturbing facts.

Clark is forced to use his powers within sight of Alicia, a new girl at school, but he is surprised to find out she has powers of her own. The two develop a bond through their shared secret, but the situation gets ugly after Alicia becomes obsessive about having to share Clark with anyone else especially Lana. Meanwhile, Lana asks Lex to investigate Adam.

When Chloe accidentally inhales a mysterious kryptonite-gas, she discovers it acts as a truth serum to anyone who comes in contact with her. She decides to take advantage of her new power by attempting to uncover Clark's secret. However, her new power comes with fatal consequences. Clark sets out to find an antidote before Chloe can discover the truth about him, rescuing her just when she's about to die.

Lawrence Garner tries to help Lex regain his lost memories. Clark tries to stop him and ends up receiving the same experimental treatment.

Kara comes to entice Clark to return to Jor-El. Jonathan reveals the deal he made with Jor-El. Lionel helps Clark discover Lex's room of obsession, and Lana leaves for Paris. Meanwhile, Lionel is denied bail, but Chloe and her father are killed in an explosion.