Clark is trapped in the Phantom Zone and with the help of another captive, manages to break free and return to Earth. Meanwhile, Zod in Lex's body, plots to destroy the Earth as Lana tries to determine if there is any of Lex left within the shell to save.
While repairing damage from Zod's attack, Clark comes down with a cold -- a cold so powerful he can blow the doors off the barn. When one of these doors nearly crushes Lois, she decides to investigate. Meanwhile, Lex tries to figure out why he's being followed by a mystery man; Lana moves into Lex's mansion but might have second thoughts.
An evil plant creature, released with Clark from the Phantom Zone, needs human males in order to reproduce and sets her sights on Jimmy Olsen. Meanwhile, Lex asks Lana to a costume party and the two of them end up consummating their relationship. Lois Lane seeks out Oliver Queen to help Mrs. Kent with some legislation and becomes attracted to him.
Clark tracks the thief who stole his mother's necklace and discovers it was The Green Arrow. Meanwhile, Lex uses his dad to test Lana's commitment to their relationship.
While attending his high school reunion, Lex and his former classmates encounter death and destruction. Meanwhile, Chloe and Clark search for escapees from the Phantom Zone, one of whom might be Raya.
Raya returns from the Phantom Zone and bonds with Clark, teaching him how to repair the Fortress of Solitude. Meanwhile, another escapee of the Zone, Baern, searches for Kal-El to revenge his time in there.
Oliver recovers from a bullet wound he received from a street punk by injecting himself with a mysterious serum that heals all wounds. Clark soon realizes he is addicted to the substance and is making him violent and careless and sets out to stop him before he hurtts anyone.
Clark goes to Seattle to track down a Phantom Zone escapee and encounters a far more menacing creature that is eventually brought down by a mysterious man. Meanwhile, Lex has been zapped into a different plane of existence -- another frequency -- and is hunted down by a man who wants to expose the goings on in the Luthor's lab. And, Lex proposes to Lana.
Clark comes across a group of illegal farm workers who are being exploited by an unknown, but powerful force. Meanwhile, Lex tries to solicit an answer from Lana concerning his marriage proposal while on a trip to Amsterdam. There, she realizes that with Lex, they can do a lot of good for the world.
Chloe discovers that The Daily Planet's gossip columnist has the ability to transform into water, and it's this skill that has allowed her to overhear many sensitive conversations, including one where Lana confesses to Chloe that she doubts her relationship with Lex because she might still have feelings for Clark. Meanwhile, Lois and Clark keep looking into the Green Arrow and begin to see a link between him and Oliver Queen.
The Green Arrow sends out for reinforcements and Bart Allan, a.k.a. The Flash, Aquaman and Cyborg return to Smallville to help him take down LuthorCorp's secret lab. During a break-in at the LuthorCorp facility, Bart is captured and tortured by Lex and Clark sets off to rescue him but is felled by meteor rock. An alarmed Chloe goes to Oliver for help and the newly formed "justice league" springs into action to rescue Clark and Bart.
After an attack by an unknown assailant, Clark awakens in a mental institution, where he is told that his notions of being Kal-El have all been a fantasy, the result of paranoid schizophrenia.
Lois puts on a love-potion lipstick made of red kryptonite and quickly lusts for Clark. She kisses him, reigniting the Dark Clark inside him. Red kryptonite-fueled Clark destroys Lex and Lana's engagement dinner and kidnaps Lana so that he can force her to be with him.
A stalker threatens Lana, causing her to seek refuge at the Kent farm. She uses the hiding time to look through Clark's stuff to learn more about him. Meanwhile, Clark helps Chloe and Jimmy get back together through discovering the stalker's identity: in this case, a member of Lex's security team. And, Lex personally invites Clark to his and Lana's wedding in order to show Clark that he has exactly what Clark wants.
Lex is working through a doctor to experiment on people affected by the meteor. The doctor is using a blind man who can see these affected people to help round them up. When Lana learns of the doctor's activities, she pleads with him not to take Clark. But the doctor isn't interested in Clark -- he's interested in Chloe.
Clark decides to tell Lana his secret on the day of her wedding to Lex which she discovers on her own; Dr. Langston knows something about Lana's baby and Lex kills him accidentally; and, Lionel Luthor threatens to kill Clark if Lana, who plans to run off to Clark, doesn't fulfill her vows to his son. She ends up going through with the wedding to save Clark who is left behind bewildered and crushed.
Clark and Chloe discover that an escapee from the Phantom Zone is a member of a super power fight club that posts its death fights on the internet, so Clark goes in and reveals his powers, hoping to fight the Zoner, named Titan.
Lex threatens to kill Chloe unless she steps aside and allows him to drug her mother, Moira, so that she can help him control the meteor freaks. When Clark catches wind of this, he offers to help Chloe bust out Moira on her own.
Lex is held captive by the wife of a Special Forces soldier who believes Lex kidnapped her husband and faked his death. She dies in a scuffle but leaves a series of explosives behind in the labyrinthine tunnels Lex is using for his secret experiments, one of which turns out to be the woman's husband.
Lana is shot at the Daily Planet and Jimmy is knocked out when trying to help find the culprit. Jimmy imagines a noir-style mystery where Lana plays a scheming wife who kills her husband, Lex, while Clark works as a reporter at the Daily Planet and Lois sings in a lounge act; and, in the real world, Jimmy and Chloe grow closer together and Clark finds out that Lana married Lex to protect him.
Lex completes work on his "super soldier" and orders him to take out a senator who knows of his laboratory. When Lois sees the soldier attack the senator, she unwittingly becomes its next intended victim. Meanwhile, Clark approaches Lana and tries to get her to leave Lex.
The Martian Manhunter tracks down a wraith from the Phantom Zone but gets wounded when he confronts it. Meanwhile, Lex and his commando unit have closed in on the wraith and attempt to capture it so that the lab can put its DNA into the genetic makeup of the Super Soldiers; Clark reveals to Lana that he's from outer space.