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.

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 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.

After being hit by a truck, John Corben becomes a human guinea pig when his heart is replaced by a machine powered by meteor rocks, which, in turn, gives him extraordinary strength, and he realizes he can use it to catch his prey...the Red & Blue Blur.

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

Tess kidnaps Lois to find out where Lois went after she disappeared for weeks. Lois's memory of the future depicts a Metropolis under Zod's rule and Clark powerless under the red sun, while Chloe forms a resistance group with Oliver. After learning of these future events, Clark makes an important decision about Zod.

A man named Sylvester Pemberton tracks down Chloe and tells her he knows about her team of superheroes and needs their help. However, before he can explain who he is, he is attacked and killed by Icicle. Clark and Chloe's investigation leads Clark to the former headquarters of the Justice Society of America, an underground team of superheros, where he meets up with Nelson (AKA: Dr. Fate), Carter Hall (AKA: Hawkman) and Courtney (AKA: Star Girl). Courtney pleads with Hawkman and Dr. Fate to help her catch the killer that is targeting their group but they are reluctant to resume their duties as superheroes. Clark, John Jones, Green Arrow and Chloe team up to help the JSA stop Icicle before he murders another member of the group. Meanwhile, Lois receives a package from a mysterious agency called Checkmate, run by the shadowy Amanda Waller.

It is Valentine's Day and while Clark is out on a date with Lois, he unknowingly becomes infected by gemstone kryptonite, which has magical wish-fulfilling properties. Clark mentions to Lois that he wishes they had a more traditional relationship, so Lois quits the Daily Planet, moves in with Clark and starts planning their wedding. Still unaware of his new power, Clark also casually tells Chloe he wishes she would spend more time watching out for him, so an infected Chloe takes his wish to heart and sets her sights on a new target: Lois. Meanwhile, Zod quarrels with Tess as well as his wife, Faora, over the construction of the new solar tower which he hopes will restore his and the Kandorians super powers which will enable them to take over the Earth.

Oliver is tortured incessantly by Rick Flag until Chloe, who used the Dr. Fate's helmet to find him, exchanges herself for him. Awakening in a secret LuthorCorp lab among partial Lex clones, Tess meets young Alexander before the bloodthirsty, dying senior knocks her down and uses Lois, who enabled Clark's healing by removing the fatal blue kryptonite, to set a sadistic trap. Despite his success, Clark lets his confidence be undermined by Jor-El in the ice fortress, but reconsiders after a pep-talk from Jonathan.

Oliver tests the Vigilante Registration Act by outing himself at a press conference, praised by the general in charge. As feared, he's tortured in a secret prison to turn on his superhero friends. Tess helps work out the design from Luthor plans for an underwater top-security facility, build in sixfold. Aquaman 'A.C.' Arthur Curry and his new wife Mera discover and penetrate the one Oliver is held in, but the general rather starts auto-destruct. Clark remains cautious and flashes to the rescue but has to deal with a specific counter-measure.

As the VRA threat intensifies, Clark takes initiative by closing down watchtower and declaring the League go officially underground, but will this be enough to stop Lt.Trotter and Slade Wilson aka Deathstroke from exposing them? Tensions rise in this mid-season finale.

After Zatanna sends a magically spiked bottle of champagne to Clark and Lois for their bachelor/bachlorette parties, the gang blacks out after the toast, only to wake up the next morning and realize they can't remember anything about the night before. While trying to retrace their steps, Lois realizes she lost her engagement ring and drags Oliver back to the Fortune Casino where she thinks she lost it. The two run into Fortune, the eccentric casino owner, who accuses them of stealing money from him. Meanwhile, Clark tells Chloe he has a memory of stealing an armored truck the night before.

Clark Kent is in nostalgic mood after Martha signs over the deed to the farm as a wedding present, wondering whether it suggests he and Lois should sell and move. Clark Luthor surprises him, using the mirror box and shattering it after having sent Kent to his world, then fool everyone for a while, in search of bloody vengeance on at least one Luthor. Kent finds himself, public enemy number one against whom everyone caries green kryptonite, at Oliver's funeral, where a bitter Jonathan scolds the 'scrooge'. Recognized and helped by the other Lois, he seeks to appease hatred and find a way back. Dr. Emil Hamilton frantically tries to repair the mirror-box, just in time.

The story of Clark Kent culminates in this two-hour series finale as Clark takes the last step to becoming the Man of Steel.