Ryan James är en liten pojke som kan läsa andras tankar, hans styvföräldrar använde honom för att råna affärer. Han lyckas smita ifrån dem men blir av en olyckshändelse påkörd av Martha Kents bil. Hon tar honom till sjukhuset, men pojken hävdar att han har minnesförlust. Familjen Kent erbjuder Ryan tak över huvudet hemma hos dem på farmen, medan de väntar på socialen. Ryan avslöjar genast Jonathans, Marthas, Lanas och Lexs innersta tankar och inser att Clark är annorlunda eftersom han inte kan läsa hans tankar. Pojkens säkerhet hotas i och med pappans återkomst, men Clark räddar Ryan, som lovar att bevara hans hemlighet.

Clark rescues Lana from the storm, but discovers that the spaceship is released, while Jonathan is buried alive with the unscrupulous reporter who discovered Clark's secret. Meanwhile, Lex is wracked with guilt over his critically injured father.

A sense of foreboding surrounds Smallville as Clark must choose between staying with Lana and his family or fulfilling his destiny to rule the Earth. Lex and Helen prepare for their marriage, and Chloe considers Lionel's offer to investigate Clark.

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.

A black kryptonite explosion splits Lex in two and his evil side - Alexander - is released. Alexander imprisons Lex in the mansion then gives full vent to his evil side - he threatens to evict Lana from the Talon unless she becomes his mate, jousts with Lionel, and tries to kill Clark and Chloe when they figure out his secret.

A krypto-mutant, Gabriel, hacks into missile codes and prepares to eliminate krypto-mutants in Smallville once and for all. A powerless Clark confronts him and is shot, and only Jor-El can save him.

Lex and Oliver Queen return to their old prep school for a reunion, but Oliver's old friends (and Lex's old enemies) start dying in mysterious accidents. Meanwhile, Clark learns that someone... or something may have left the Phantom Zone with him.