Metropolis, three months later. Clark Kent (under the influence of the red kryptonite ring) has becomes a criminal, heisting banks, going to night-clubs, and living under the alias 'Kal'. But he comes into conflict with not only his Kryptonian-marked chest, but a ruthless and greedy gangster, named Morgan Edge, who wants an ever increasing percentage of the stolen loot, and also begins to suspect Clark's alien origins. Meanwhile, Lex Luthor is declared dead, but he is living with the weird Louis Leery Jr. in an isolated desert island. Back in Smallville, Dr. Helen Bryce comes to his funeral and meets Lionel Luthor in the mansion where secrets are disclosed. Lana Lang and Jonathan Kent try to bring Clark back to Smalville. Unsucessful after Lana's pleas to Clark, Jonathan makes contact in the cave with the spirit of Jor-El who imbues Jonathan with Kryptonian super-powers to combat Clark and bring him home... in exchange for a price. Also, Chloe enjoys her new job at the Daily Planet, while tailing Lana during her search for Clark.

Lex returns to Smalville and the Lex mansion, and invites Dr. Helen Bryce for a second honeymoon while trying to find out if it was her or his father who attempted to kill him. Meanwhile, Clark also returns to Smallville and the Kent farm, but Morgan Edge finds him and threatens to kill Jonathan and Martha in to get what Clark stole from Lionel Luthor's safe, which is the stolen vial of Clark Kent's blood. With the financial status of the Kent family in dire straights, the farm is sold in an auction, but there is a surprise in the end. Also, Lana tries to declare her love for Clark, but he rejects her love out of fear that she may discover his secret. Clark also returns to Smallville High and to the Torch newspaper under Chloe who continues to investigate Clark's origins.

The aftermath of Doomsday's attack on Chloe and Jimmy's wedding leaves Clark in shock, but before he can search for the kidnapped Chloe, an evil being, known as The Persuader, appears and attacks him. Rokk, Imra and Garth, also known as The Legion, step in from the future to help vanquish the Persuader and the group realizes Brainiac has taken over Chloe once again. Meanwhile, up at the Fortress, Chloe, as Brainiac, informs Davis he is Doomsday and was created to kill "the other Kryptonian" and destroy the world.

Clark decides that he is ready to start his training at the Fortress of Solitude to become 'Superman'. However, the spirit of Jor-El insists that he return to Metropolis to cut his ties with the people he knows before he begins. Lois reappears in the city with no recollection of vanishing to the future. Her investigation into a monorail crash brings her into contact with a new reporter named John Corben. John is opposed to the "Red and Blue Blur", and has a secret power and identity himself. Meanwhile, Chloe's friendship with Clark deteriorates when he refuses to use the Legion ring to go back in time to save Jimmy. Elsewhere, Oliver turns down a dark path in his quest to rid the world of evil. General Zod makes his entrance at the Luthor mansion before Tess.