Clark manages to escape from the Phantom Zone with the help of an unexpected ally. He subsequently sets out on a mission to hunt down the dangerous prisoners who followed him to Earth. Adding to Clark's troubles, there is a new vigilante in town who goes by the name Green Arrow. Meanwhile, Lex and Lana take the next step in their relationship. As the season progress, the rivalry between Clark Kent and Lex Luthor will explode into a fierce good-versus-evil battle.
A powerless Clark is trapped in the "Phantom Zone" surrounded by the criminals his father imprisoned there. However, an unexpected ally comes to his aid. Meanwhile, Zod in Lex's body advances his plan to transform Earth into a new Krypton, while using Lana to produce an heir.
In the aftermath of Zod's activities, Clark develops a new power. Lois gets a new job, Lana takes a new step in her relationship with Lex, and Lex has to deal with a new danger. Meanwhile, an old friend of Lex's arrives in Metropolis.
Clark and Chloe pursue a plant creature that uses male humans to recreate, one which has taken Jimmy Olsen as its next human breeding ground. Meanwhile, Oliver Queen asks a reluctant Lois to be his date at a charity ball held by Lex.
The mysterious Green Arrow steals a necklace from Martha, and both Lois and Clark resolve to find out who the vigilante is. While Clark determines Green Arrow's true identity, Lex continues his investigation of the mysterious black box while Lionel warns Lana against him.
Lex and Oliver Queen return to their old prep school for a reunion, but Oliver's old friends (and Lex's old enemies) start dying in mysterious accidents. Meanwhile, Clark learns that someone... or something may have left the Phantom Zone with him.
After escaping from the Phantom Zone, Raya comes to Smallville to visit Clark. Raya and Clark grow close, and Raya reveals how to repair the Fortress of Solitude. Unfortunately, Baern, another escapee seeks out revenge on Clark and Raya for his time spent in the Zone.
After being shot while stopping a carjacking, the Green Arrow begins acting strangely. Chloe and Clark investigate and find Oliver is taking a super drug that while healing his wound, has some dangerous side effects.
One of the escapees from the Phantom Zone has killed the crew of a ship in Seattle. Clark confronts the killer who feeds on the bones of his victim. In Smallville, a patient in LuthorCorp Labs escapes experimentation and seeks revenge on Lex by trapping him in a dimension where he can see and hear those around him, but they cannot see him.
An illegal immigrant comes to Clark for help, escaping from a nearby farm where he's working... a farm that houses a dark secret.
A Daily Planet gossip columnist uses her special power to overhear a conversation between Lana and Chloe, and publishes the conversation... where Lana admits having doubts about marrying Lex. While Chloe investigates the reporter, Lois asks Clark to help her investigate the mysterious Green Arrow bandit when she suspects he may be Oliver Queen in disguise.
When Lex's Level 33.1 project comes to fruition, Oliver Queen must bring together several of Clark's "heroic" super-powered allies together: Arthur Curry, Bart Allen, and Victor Stone.
Clark is in his barn one moment... and the next finds himself in a psychiatric hospital where he discovers he's been suffering from delusions that he came from another planet and has super-powers.
Clark is once again exposed to red kryptonite, and his "other self" goes on a rampage of sorts on Valentine's Day, kissing the women he's most attracted to and expressing his uninhibited feelings for the various relationships around him.
Lana has a stalker which leads her to an unexpected hideout. Also, Chloe has to reevaluate her feelings for Clark after she and Jimmy break up due to Jimmy's belief that she isn't really over Clark.
A boy named Tobias was blinded by the meteor shower but given the ability to identify other meteor freaks. Lex is using Tobias to locate other people with abilities so that he can perform experiments on them. Lana learns of Tobias and is fearful that he will name Clark as a freak, so she offers him a cornea transplant to keep him quiet. But Tobias has some surprising news.
Clark has second thoughts about Lana marrying Lex, and Lana has the same concerns. Meanwhile, the doctor involved in the secret behind Lana's pregnancy threatens Lex with his knowledge.
Clark and Chloe find an escaped Zoner named Titan who is the star of a secret fight club that puts its death battles on the internet. Lois can tell that there is a story and goes to investigate, where she is put in the ring to fight. Clark goes in as a super-powered fighter to take on Titan but ends up against a different opponent instead.
Lex discovers that Chloe's mother has special abilities and forces her to help him in exchange for Chloe's life. However, she has a trick or two of her own to use to escape.
Lex and Clark get a chance to hash out their differences... when they're both trapped in a cave after an explosion, and Clark is unable to get them out without revealing his powers.
Lana and Lionel have a secret meeting, after which Lana is shot. While Jimmy is observing photos of the encounter, he is knocked unconscious. While unconscious Jimmy dreams about what life in Smallville would have been like in the 1940s. Clark is a reporter at the Daily Planet, Lana is a siren who planned the demise of her magnate husband Lex, and Lois is a singer at a bar that Lionel owns.
Lex tries to turn a soldier that supposedly died in Afghanistan into a "super-soldier." A senator threatens to tell the world about Lex's labs, prompting Lex to send the "soldier" to kill the senator. Lois sees the attack and becomes the soldier's next victim.
Clark discovers the reason Lana married Lex then and sets out to kill Lionel. Lex tries to use DNA from the last phantom to power his super-soldiers. Lois goes to a dam to search for Lex's lab but is caught by a security guard and fatally injured. Chloe's power is discovered.