Clark learns that John Jones was shot while working as a police officer; Lana tells Tess that Lex isn't the man she thinks he is, forcing Tess to re-evaluate her position as head of Luthercorp.

Clark discovers that Davis is still alive and confronts Chloe about protecting him. Oliver discovers Jimmy breaking into Chloe’s apartment, but things get rapidly worse after Davis jumps from the shadows and attacks both of them.

Chloe returns and begs Clark to kill Davis, claiming he can no longer keep the beast under control. Tess has assembled a team of meteor freaks, including Plastique, to track down Davis so Clark can kill him. However, things get out of hand once Tess’ team discovers she is double-crossing them.

Clark tells Jor-El he’s ready to start his training, but Jor-El sends him back to Metropolis to cut ties with Lois before he can begin. Chloe is shocked when Lois suddenly reappears after having been missing for weeks, but Lois has no recollection of vanishing into thin air with the Legion ring. Chloe begs Clark to use the Legion ring to go back in time to save Jimmy, but he refuses, driving a wedge into their friendship. Meanwhile, Zod arrives at the Luthor mansion...

After being struck by a truck, John Corben wakes up alone in an abandoned apartment as a man-machine with a Kryptonite heart. Corben realizes he now has superhuman strength and sets out to exact revenge on the Red-Blue Blur, who he perceives to be an irresponsible vigilante. Against Clark's wishes, Lois involves herself in the Red-Blue Blur's investigation, and winds up getting kidnapped by Corben.

Zod and his soldiers release a virus into the air that turns humans into zombies. The only way to stop it is to make an antidote from the blood of another Kryptonian. After Lois is infected, Chloe pleads with Clark to donate his blood to stop the epidemic, even though it risks outing him to Zod.

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 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 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.

Lois finds Clark's lifeless body and removes the blue kryptonite enabling him to heal himself. However, Lois sneaks away before Clark fully awakens in order to protect his secret. Meanwhile, Chloe is desperate to find Oliver, so she turns to an unlikely source for answers. Jonathan returns to the Kent Farm with a message for Clark, and Tess awakens in a LuthorCorp lab.

In an effort to protect the rest of the team, Oliver decides to register for the Vigilante Registration Act to see what the government plans to do with the new law. As he suspected, it was a trap to lure superheroes to an undisclosed location where he is confined to a jail and subjected to a battery of brutal tests under the supervision of Col. Slade. Aquaman and his new wife Mera team up with Clark to free Oliver. Lois is frustrated when Clark continues to push aside her offers to help the team and sets out to prove she can play with the big boys.

The VRA is in full effect and things take an unfortunate turn of events after the Green Arrow tries to stop a mugging but is attacked by citizens for being a super hero. Clark discovers that the civilians who attacked Oliver were all marked with a darkness tattoo. Carter Hall and Star Girl return to help Clark deal with Slade’s re-emergence after he kidnaps Lois.

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.

Clark is shocked to find a mirror box in the barn. Clark Luthor surprises him and sends Clark Kent back to the alternate reality where Clark runs into a very angry Jonathan Kent. Meanwhile, back in our reality, Clark Luthor visits Tess and tells her that if she doesn’t side with him he’ll kill her. Lois asks Emil to help her bring Clark back.