Clark returns to Smallville as Kal-El - intent on fulfilling his destiny, he goes after a powerful kryptonian crystal that Lex has obtained in Egypt. Meanwhile, newcomer Lois Lane arrives in Smallville to look into the death of her cousin Chloe, and Lana returns from Paris with a new boyfriend. Jonathan lies in a coma after the events of last year's season finale and Lionel must deal with his new life in prison.

Clark is drawn to the state penitentery by one of the kryptonian crystals, which Lionel is using to switch bodies with Lex. Clark intervenes and Lionel enters his body instead. While Lionel uses his newfound super-powers to regain his lost fortune and alienate Clark's friend, Clark must convince his parents that he is the "real" Clark and reverse the processs, while avoiding murderous convicts.