Thrown into the Phantom Zone, a Kryptonian jail created by Jor-El, Clark finds himself without powers and surrounded by revenge-seeking criminals sent away by his father. Meanwhile, having taken over Lex's body, Zod keeps Lana captive with a demand to sire him an heir and begins his plans to turn Earth into a Krypton-like planet using the alien ship's hard drive. After Lois and Martha's plane crashes near the Fortress of Solitude, Jor-El tells Martha how to kill Zod. Back at the Daily Planet, Chloe reunites with an old flame, Jimmy Olsen.
Clark works hard to clean up the destruction done by Zod and develops what he thinks is his first cold. However, he soon discovers it is a new power, super breath! Lois lands a job at The Inquisitor, the local tabloid, and Lana moves in with Lex, who believes someone is following him, which quickly proves to be true after he is kidnapped.
Still guilt-ridden about the destruction he caused while he was Zod, Lex throws a charity costume ball for the town and hires the All-American Rejects to perform. Meanwhile, Clark and Chloe pursue a creature who uses male human bodies as potting mix to procreate, and the hunt intensifies after the creature gets hold of Jimmy Olsen. Lois reluctantly agrees to be Oliver Queen's date to Lex's ball.
While attending a fundraiser, Lois witnesses the Green Arrow steal a rare diamond necklace off Martha's neck and vows to find the man behind the costume. Clark does some investigating of his own and discovers Oliver Queen is the Green Arrow and has been stealing from the rich and giving to the poor. Meanwhile, Lex enlists Lionel's help in testing Lana's loyalty.
As teenagers, Lex and Oliver went to the same prep school, where Oliver and his friends bullied Lex and his friend Duncan. Lex eventually turned on Duncan to gain their acceptance, prompting Duncan to throw himself in front of a moving car. Lex and Oliver return to the school for a reunion and are startled when Oliver's old pals are killed in violent and mysterious accidents that point to Duncan. Meanwhile, Clark sees satellite photos that show four other craters were created the day he escaped from the Phantom Zone, causing him to believe that others may have followed him.
Clark is thrilled when he learns Raya managed to escape from the Phantom Zone and has come to see him in Smallville. The two grow close and Raya shows Clark how to restore power to the Fortress of Solitude. However, Baern, a killer who also escaped from the Phantom Zone, takes on both Raya and Clark as he seeks revenge for his imprisonment.
Clark discovers the Green Arrow was shot while trying to save a couple from a carjacking, but Oliver denies he was injured. However, when Oliver starts displaying erratic behavior, Clark and Chloe investigate and discover he is taking a super-drug that causes his body to heal itself but has severe side effects. Meanwhile, Lana makes a shocking discovery that will impact her relationship with Lex.
Clark learns a Zoner has landed in Seattle and slaughtered the entire crew of a working ship. Upon investigation, Clark comes face to face with a horrifying phantom who sucks the bones out of people. Meanwhile, a patient with the ability to morph into different frequencies escapes from LuthorCorps' secret experimental lab and seeks revenge on Lex by imprisoning him in another spatial period where he can see and hear everyone but no one can see him.
Clark is shocked to discover his neighbor Jed McNally is holding migrant laborers captive and forcing them to work on his farm. Feeling guilty since he sees himself as the ultimate illegal immigrant, Clark seeks help from Martha to allow a young boy and his mother to stay in the country.
After Lana confesses to Chloe she has reservations about marrying Lex due to her lingering feelings for Clark, The Daily Planet gossip columnist, Linda Lake, runs a story detailing their exact conversation. Determined to prove she didn't give the story to Lake, Chloe investigates her fellow co-worker and discovers she has the ability to turn herself into water and uses it to secretly overhear conversations for her column. Meanwhile, Lois begins to suspect Oliver is the Green Arrow and enlists Clark's help to prove it.
The Green Arrow sends out for reinforcements and Bart Allen, 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.
Clark is attacked and wakes up in a mental asylum where the attending physician, Dr. Hudson, tells him he has been there for five years due to his elaborate fantasy that he has alien superpowers. In this new world, Martha is married to Lionel Luthor, Chloe is deemed insane, and Lana chose Clark over Lex. Lana begs Clark to agree to Dr. Hudson's treatments so they can be together, but when a fellow patient named John, a.k.a. Martian Manhunter, tells him the good doctor is actually a phantom and he needs to kill him in order to return to reality, Clark must make the toughest decision of his life.
After Lois tries on lipstick made with red kryptonite, she becomes overwhelmed with desire for Clark and makes her move. The two share a kiss, transferring the red kryptonite to Clark and his inhibitions immediately shut down causing "bad-Clark" to emerge. Fueled by the red rock, Clark decides to break up Lex and Lana's engagement dinner and kidnap the bride-to-be.
After receiving a photo of herself dressing in her room, Lana realizes she has a stalker and decides to hide out at a surprising location. Meanwhile, Jimmy breaks up with Chloe because he believes she isn't truly over Clark, forcing Chloe to take a deep look at her feelings for her best friend.
Clark and Chloe discover that Tobias, a young man who was blinded in the meteor shower and now has the ability to identify "meteor freaks," is being used by Lex to locate people with abilities in order to experiment on them. Lana finds out about Tobias's gift, and fearing he will name Clark as one infected, offers him a cornea transplant in exchange for his silence. However, she is not prepared for Tobias's shocking news.
On the day of Lex and Lana's wedding, Lex receives a call from Dr. Langston who threatens to tell Lana the truth about her baby. Lana begins to have second thoughts about marrying Lex and Clark comes to his own realization that he can't let Lana marry Lex and decides to tell her about his secret. However, no one is prepared for what happens when Lionel Luthor steps in.
Clark and Chloe discover Titan, a Zoner, is the star of a secret fight club whose bloody battles to the death are broadcast on the internet. Lois smells a story and decides to investigate on her own but is captured and forced to participate in the fights with Athena as her first opponent. Clark reveals his powers so he can fight Titan but is stunned when he is thrown in the ring with Lois instead.
After Lex discovers Chloe's mother Moira has the power to control meteor freaks, he develops a drug to wake her from her catatonic state in the asylum, then threatens to kill Chloe unless she uses her power to help him. Clark helps Chloe break into the asylum to rescue Moira and finally get to know her mother.
After Jodi, the wife of a Special Forces soldier, sets off a pipe bomb in one of Lex's secret labs, Lionel is severely injured and Lex is taken hostage by the enraged spouse. Claiming Lex kidnapped her missing husband, Jodi threatens to blow up the entire lab with Lex inside unless he tells her where her husband is. Clark sets off to rescue Lex, but is immediately felled by the kryptonite lining the earthen walls. Lex and Clark realize the only way they will make it out alive is by helping each other.
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 1940s version of Smallville in which Lana is a femme fatale who orchestrated the murder of her tycoon husband Lex, Clark works at the Daily Planet as a reporter, and Lois is a sultry singer working at a bar owned by Lionel. Meanwhile, back in 2007, Clark discovers why Lana married Lex.
Lex has been secretly trying to turn Wes Keenan, a military man who supposedly died fighting in Afghanistan, into a "super soldier" by injecting him with DNA pulled from the various meteor freaks he has captured. After a crooked senator threatens to expose his secret labs, Lex dispatches Wes to kill the senator, but Lois witnesses the attack and inadvertently becomes the super soldier's next target. Meanwhile, Clark tries to convince Lana to leave Lex.
When Clark discovers Lionel threatened to kill him unless Lana married Lex, he goes after Lionel to silence him once and for all. Lana tells Lex she is leaving him, and Martian Manhunter makes a return appearance to help Clark stop Lex, who is trying to find the last wraith from the Phantom Zone in order to use its DNA to power his army of super soldiers. Meanwhile, Lois goes to Reeves Dam in search of information about Lex's secret lab and is brutally stabbed by a security guard. Chloe's secret power is revealed.