Clark decides that this year will be the year of Clark and he will not be worried with what Jor-El has in store for him anymore. Clark goes out for the football team, goes through rocky terrain with his relationship with Lana, sees his relationship with Lex begin to fully crumble, meets future superheroes and old obsessions, and battles witches from the 17th century just in time to graduate from Smallville High. Clark's true destiny is also revealed to him by the season's end, and a second meteor shower comes to Smallville.
Clark and Lois search for Chloe. They discover that Lex and General Lane have had her hidden away, but Lionel manages to send Trent MacGowen to kill her. Meanwhile, Lana returns to Smallville and Jason follows her.
Abigail Fine receives kryptonite-enhanced plastic surgery to treat her acne, but suffers from the side-effect of inflicting those she kisses with life-threatening hallucinations. Clark joins the football team. Lana is attacked. Lex learns that Lana is dating Jason.
Clark and Lois discover that the cheerleaders are spiking the football players sports drink with a kryptonite-enhanced love potion. Lex tries to patch things up with Clark by handing over the research he had on him.
Clark is drawn to the prison where Lionel is being held. When he sees Lionel attempt to stab Lex with a strange glowing stone, Clark grabs for the stone causing the two men to switch bodies. Learning his new body has super powers, Lionel immediately begins wreaking havoc on Smallville. Trapped without his powers, Clark must figure out a way to get his body back in order to save his friends and family.
Chloe investigates an underground gambling ring at school run by foreign exchange student Mikhail Mxyzptlk. Mxyzptlk uses his telepathic powers to manipulate the football games. Under Mikhail's influence, Clark injures another player. Lex reveals to the school board that Jason is dating Lana, then he takes Mikail to Level Three.
Clark helps Lex discover the truth when Lex is accused of killing a one night fling. Meanwhile, Lana sees Genevieve Teague in a dream of Isobel Thoreaux's execution just before she arrives to meet her son's new girlfriend.
A LuthorCorp experiment is released into the atmosphere- a toxin that causes its victims to hallucinate their worst nightmares. Chloe, Clark, Lana, and Jason all fall victims to the toxin. Lex, desperate to find a cure, takes a dangerous antidote. Meanwhile Genevieve Teague arranges for Lionel Luthor's release from prison and Chloe finds her mom.
Claiming to be cured, Alicia Baker is released from Belle Reve hospital and comes to Smallville to rekindle her relationship with Clark. Initially skeptical of Alicia, Clark finds himself enjoying dating someone who knows his secret, but when she pushes for more, he hesitates, causing her to use red kryptonite on him.
Clark has big concerns after Alicia becomes the prime suspect in a brutal attack against Lana and Jason. Clark initially defends Alicia, but when the evidence begins to pile up, he is forced to take a harder look at the situation. Hurt by Clark's actions, Alicia forces Clark to unknowingly reveal his powers in front of Chloe.
Clark is approached by Met U for recruitment and meets Geoff, a former Smallville resident. It soon becomes apparent that he is using his powers to paralyze anybody who gets in his way... including Lois.
Lois accidentally hits a dog and brings it back to the farm to heal, but Clark quickly realizes it has super-strength. He investigates and discovers it was part of an aborted LuthorCorp experiment and that robbers are using the dogs to help them steal money.
After Clark receives a message from the recently-deceased Dr. Swann, he and Lana follow Jason and Lex to China in search of one of the Stones of Power. Lana is tortured, causing Isobel to emerge and wreak havoc in her search for the crystal.
Lucy Lane, Lois' younger sister, comes to Smallville but Clark catches her stealing money from the Talon to pay off a European loan shark. Lex offers to help but everything is not what it seems. Meanwhile, a thief breaks into Lana's apartment and steals the crystal; Jason suspects Lionel.
A glimpse of the future Lex Luthor is revealed after a kryptonite explosion splits Lex in two and his evil side - Alexander- is released. Alexander immediately imprisons Lex in the mansion and begins his rampage by trying to kill Clark and Chloe Sullivan in the lab, jousting with Lionel and convincing him to return to his dark seeded nature, and finally, threatening to close the Talon unless Lana moves in with him.
On the eve of the Smallville High School Prom, stuck-up candidate for Prom Queen Dawn Stiles is involved in a car crash into a ravine filled with chunks of kryptonite. While her body lies in a coma, Dawn finds her spirit allowed to possess the bodies of others, where she can continue her quest to become Prom Queen.
Kevin Grady, a boy who can cause people to temporarily lose their memory, turns his powers on Clark and causes him to have total amnesia. Chloe discovers what has happened and must teach Clark about his superpowers while simultaneously trying to keep him from accidentally revealing them to others. Clark meets Lana and falls in love all over again. Lex takes advantage of the situation and convinces Clark to tell him about a secret room behind the back wall in the Kawatche Caves.
Checking out a crater in a cornfield, Clark and Lana discover a baby with no parents and take him back to the Kent farm. However, when the baby, Evan, ages from a newborn to a 7-year-old in less than a day, it becomes clear he is aging at a rapid rate and they turn to Lex for help. Meanwhile, Lionel vies for one of the stones.
Clark must stop the school photographer after he sets up a fake high school and uses his ability to petrify people to kidnap students- including Chloe and Lana- to keep the glory days of high school going forever. Meanwhile, Lex and Lionel are kidnapped and tortured by the Teagues in an effort to find the Kryptonian artifact, revealing that Lana has it.
Allison Mack did not appear in the opening credits of the first episode during its original airing. This was a tactic to maintain suspense of Chloe's fate, as she had been shown to be caught in an explosion in Covenant. She is not confirmed to be alive until the end of the season premiere, Crusade. She does appear in the opening credits of every other episode and reruns, after Jensen Ackles.
Jensen Ackles appeared in 20 of 22 episodes this season (Onyx and Ageless being the exceptions.) This was the only season that he appeared on Smallville.
This is the last season with this style of opening credits.
This is the first season to have both first-and-last episodes starting with the same letter (Crusade, Commencement)
This is also Jonathan Kent's last full season; he would appear only half of the fifth season, to die in the episode Reckoning.
Chloe discovers Clark's secret this year. This makes her the second regular cast member to discover Clark's secret (the first being Pete Ross), and the first cast member to be aware of the secret before Clark confesses. (Pariah)