Lex is targeted by a former Belle Reve patient who can move through frequency, and who wants him to come clean about 33.1. Meanwhile, Clark goes to Seattle to hunt down one of the Phantom Zone escapees.

Clark enters a parallel environment in his subconscious where he is powerless, no one believes the truth about him, and things have turned out much, much differently.

After a secret meeting with Lionel, Lana is shot at the Daily Planet by a mysterious gunman. Jimmy is knocked out while studying photographs of the scene and dreams about a 1940, black-and-white version, of Smallville. Jimmy finds himself playing the role of a reporter with Chloe his secretary, and a bumbling Clark also works there, as his sidekick. Jimmy's investigation leads him to Lana, who turns out to be a very evil femme fatale who plans to orchestrate the murder of her tycoon husband Lex by using Jimmy as the patsy. Jimmy's research further takes him to a notorious nightclub owned by Lionel Luther, and Lois is a sultry singer working at club who is having a fling with Lex to help him orchestrate the murder of Lana. Meanwhile, back in 2007, Clark discovers why Lana married Lex after Chloe learns it from Lana. Also, Lois further meddles in the shooting case by stealing a silver-lined cigarette case which holds a clue.

Clark's first day on the job at the Daily Planet begins with a bus exploding right outside the building, which leads him and Lois on a trail of someone who might be infected by kryptonite. Chloe finds a runaway teenage girl, named Bette, whom Chloe suspects is involved in the explosion when Bette (whom will later become the fire-starter Plastique) has the meteor-rock power of pyrokinesis. In the meantime, Chloe also meets a local medic, named Davis Bloom, who takes an interest in her, even though she's engaged to Jimmy Olsen. Elsewhere, Tess meets Clark for the first time as she takes over the Daily Planet in Lex's absence and immediately senses something not right about him.

Clark and Chloe search for Lana, who has it in her head that things will be better between her and Clark if they were on "a more-even keel," and goes off on her own in search of a suit developed by Luthor, Corp. that will make her invincible.

All signs point to the fact that Clark was not the only one that landed on Earth the day of the meteor shower in Smallville.

Chloe mysteriously returns to Smallville where she gives Clark the idea of killing Davis by telling him he can't keep the beast under control. Unknown to Clark, Tess has gotten together a kill-team affected by meteor rocks to track down Davis so Clark can kill him, but things get out of control when Tess' team discovers that she betrayed them. Meanwhile, Oliver, as the Green Arrow, agrees to help Clark look for things that can stop Davis by breaking into Tess' safe at the mansion to steal some black Kryptonite hoping to separate the two entities apart, while Chloe is revealed not who she appears to be, and Tess is working for another greater power beyond everyone else.

Clark tells Oliver that he must kill Davis, but Clark deals with the fact that he can't take a human life. This leaves the justice league to take the affair on their own hands. Then, Rokk Krinn teleports from the 31st Century to give Clark another Legion time-traveling ring so Clark can exile Davis/Doomsday to the future. But in a surprising twist, Lois confronts Tess about her nefarious plans involving a mysterious crystal and in the fight, Lois accidentally finds Rokk's ring, and gets zapped into the future. Meanwhile, Chloe gets in the middle of Clark and Oliver's fight about Doomsday's human carnage, in which Dianah/Black Cannary and Bart/Impulse intervene. Jimmy finds out Clark's identity, leading to a fateful showdown when Clark attempts to use black kryptonite to split Davis from Doomsday and seal the beast in a large hole in the ground. But nobody is prepared for what Davis will do afterwords.

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.

Clark, unknowingly, exposes himself to Zod when a virus is released on Metropolis that turns its residents into zombies.