It's been four weeks since the Fortress collapsed and Clark disappeared. Green Arrow calls upon Black Canary and Aquaman to locate the missing Clark Kent. Clark, in the meantime, is powerless and residing in a Russian prison camp in Siberia. With Lex Luthor missing and presumed dead, a new ruthless CEO, named Tess Mercer, is appointed the head of LuthorCorp and moves into Lex's mansion with her own dark plans for Clark and Metropolis. Chloe is kidnapped by a clandestine group that has discovered her special powers and they want to test the limits of those new powers by locating Green Arrow and his friends.

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.

Oliver Queen is poisoned at a charity fundraiser and Clark races around the world to find a cure.

When Tess inadvertently activates the mysterious Kryptonian Knowledge crystal found in the Artic, it emits a high-band beacon which summons an alien queen, named Maxima, who arrives on Earth and begins a search for her new mate, with a kiss that is too strong for humans to survive. Meanwhile, after just moving in together, Jimmy finds a letter that Chloe wrote for Clark that revives Jimmy's insecurities.

After Jimmy and Chloe disappear from sight for a bit and it turns out it has been against their will, Lois and Clark pose as a couple to flush out the kidnapper.

A serial killer is on the loose in Metropolis, and Clark always seems to be one step behind him, while Chloe's paramedic friend seems to think he blacks out and performs the dirty deeds, himself.

Jimmy takes a photo of Clark using his super-speed while saving Lois from danger, but it comes out blurred. Tess decides the story should make the front page for the Daily Planet exposing the mysterious new 'superhero' that. Chloe refuses to continue helping Clark protect his secret, so Clark turns to Oliver for help when Jimmy gets too close to discovering his secret. Meanwhile, Lois meets Sebastian Kane, a new reporter at the Daily Planet, who has the power to see peoples' memories by merely touching. He has been hired by Tess to find the missing alien crystal.

Clark receives a crystal that sends him and a visiting Lois to the Phantom Zone where they run into Kara. Kara tries to open a portal for Lois before it's too late but Zod's wife, Faora, manages to escape in Lois's body and proceeds to go on a rampage through the streets of Metropolis.

When Chloe begins having memory loss when the essence of Brainiac begins replacing her memories with Kryptonian codes, Clark decides to use the Crystal of Knowledge to reconstruct the Fortress of Solitude and ask the spirit of Jor-El for help. Meanwhile, Jimmy begins to worry about Chloe's well-being, while Davis, disturbed by the knowledge that he may have alien origins, begins to become drawn to Chloe.

Oliver gets a step closer to finding Lex, but Clark refuses to help for the time being, due to Chloe's special day, while Lois finds she has special feelings for Clark, who has a surprise (or two) waiting for him at the wedding reception.

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 discovers John Jones was shot while working as a police officer, so Clark dons the uniform and goes undercover to find the culprit. Meanwhile, Lana confronts Tess and tells her Lex isn't the man she thinks he is. Lana's shocking news forces Tess to reevaluate her position as the head of Luthorcorp.

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.

There is an explosion at Luthorcorp when Oliver is about to announce he controls the interests of Luthorcorp. Oliver suspects Lex is behind the explosion but he realizes the bomb was made by an ex Queen Industries' employee called Winslow Schott. Lana learns her power suit gives her the power to absorb Kryptonite.

Linda Lake comes back to Smallville and blackmails Clark to expose his true identity. However, Clark decides he will reveal his secret by himself. A fanatic teenager fakes a fall so Clark can save her.

Tess devises a plan which will reveal Clark's true identity, while Davis comes up with a plan to ease the demon within him, but finds himself trying to scramble after Jimmy sees him kill someone.

Reflecting on her status in life, Chloe finds that she's not all what she dreamed of becoming, so when a magician asks her to make a wish, little did she dream of it coming true...becoming Lois.

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 and Lois are attacked by two thugs which one of them is hit by Lois with her heel, she starts feeling a bit heroine about it so she recruits Jimmy for the picture so she can convince the people she is Metropolis' new hero, with the name of 'Stiletto', so she can take away the famous red and blue blur. However, Lois may end having contact with this red and blue blur when Clark wants to try to track down the mysterious 'Stiletto'. While Clark tries to help Chloe recover her stolen laptop computer with all of the Justice League's files on it, she continues to hide Davis in the basement of The Talon. Elsewhere, Jimmy is working as a bartender at a nightclub where the thugs who robbed Chloe and Lois reside and are plotting to kill Stiletto to reclaim the city for themselves.

Davis asks Chloe if she can go away from the city with him, but when Clark realizes Davis is alive, he confronts Chloe to give him an explanation about it. Meanwhile, Oliver discovers that Jimmy has become a pill-popping junkie and offers his services and emotional support. But Jimmy is too consumed by his anger and paranoia and brushes off Oliver. Later, when Oliver sees Jimmy breaking into Chloe's apartment to steal money and items to buy more drugs, things get worse when Davis appears and attacks them both. It leads to an angry Clark tracking down Davis/Doomsday to the ruins of the Fortress of Solitude for a brutal confrontation.

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.