After Clark rescues Lana from the eye of the storm, he discovers the storm's wrath has unleashed the spaceship into the fields and buried his father alive along with the unscrupulous reporter who has discovered Clark's secret. Meanwhile, Lex is wracked with guilt over his father.
Clark goes into hiding after he discovers a startling new power that quickly gets out of control and almost burns Lana. However, after a hot new teacher uses kryptonite-enhanced pheromones to convince Lex to marry her, then spellbinds Jonathan, Clark must get a grip on his new power in time to keep Jonathan from killing Lex.
After one of Clark's friends discover the spaceship in the cornfield, Clark goes against his parents' wishes and reveals his secret, but is shocked when the reaction he gets makes him question his friend's loyalty.
The school unknowingly uses red kryptonite in the class rings and its effect on Clark stuns his friends and family as he turns into a rebellious and dangerous teenager who does not care about showing off his powers. Jonathan and Martha scramble to find the truth behind Clark's behavior before he exposes his true identity, while Lana finds herself drawn to the "new" Clark who declares his love for her.
Clark is concerned when he discovers someone has been leaving love notes for Lana at her parents' grave and warns her to stay away from the mysterious poet. Fed up with Clark's over-protectiveness, Lana follows the dark and handsome stranger to his home and discovers his parents keep him locked in chains. Unable to leave him like that, Clark and Lana break into the house to save the boy, but soon realize why he was locked up in the first place.
After realizing the farm is in financial trouble, Martha goes to her estranged father for help. Clark is thrilled at the prospect of meeting his grandfather but Jonathan's refusal to see the man prompts Clark to force a reunion that doesn't go exactly as planned. Meanwhile, Lana discovers an old photograph that suggests her father may still be alive.
A mysterious woman shows up claiming to be Clark's mother, prompting the Kents to tell Clark what happened after they discovered him in the cornfield that fateful day. Clark discovers why his father hates the Luthors, how his adoption was fixed, and who really rescued Lex from the edge of death.
When Clark tries to warn Lana and Chloe about Ian, an overachieving student who is surreptitiously dating both girls, they accuse Clark of jealousy but realize too late that he was right. Meanwhile, frustration with his father causes Lex to lose his temper and attack a parking attendant's car with a golf club, landing him in an anger management class where he meets an interesting new woman.
While moto-crossing with Pete, Clark falls into a cave and discovers two hidden treasures - ancient Indian writings that hold the key to his identity, and a beautiful girl whom he believes to be his soulmate. Desperate to preserve the writings, Clark pits father against son as he enlists Lex's help to stop Lionel's construction crew from demolishing the cave.
Whitney returns home from the Marines looking to rekindle his relationship with Lana but his suspicious behavior prompts Clark to question his true motives, ultimately revealing a shocking truth about "the new Whitney." Lex becomes suspicious of his new girlfriend after he discovers a questionable photo of her with Lionel.
After Lex discovers that Lionel installed cameras in the mansion, he hires some thugs to bug Lionel's office, but things get out of control when Lionel and Martha surprise the thugs and are taken hostage. Clark must figure out a way to save his mother without exposing his powers and sees his chance on an adjacent tall building - if only he could make the leap in a single bound.
When Lionel is shot, Jonathan is arrested, but after Clark and Pete perform their own crime scene investigation, they realize that more than one person had the opportunity to kill Lionel - including Lex. Meanwhile, Lana is suspicious after she asks her father to take on Jonathan's case and he declines for mysterious reasons.
After Pete and Chloe are infected by a parasitic worm, it turns them into thrill-seeking daredevils and Pete uses red kryptonite to get Clark to join them on a dangerous adventure. Not only does Clark show off his powers, but he kisses Chloe in front of a stunned Lana.
Lex finds Lucas, the son Lionel gave up for adoption, and brings him home in the hope that the two of them can unite against Lionel. When Lionel's machinations end up putting all three of them in a dangerous situation, Lex is left to wonder whom he can really trust. Meanwhile, Clark decides to take a job at the Talon.
Clark rushes to find an antidote after Martha is infected with a toxic virus and falls into a coma, but when Clark also falls ill, it is up to Jonathan to find a cure in time. To further complicate things, Dr. Bryce demands an explanation from Jonathan when he refuses to let her treat Clark.
Determined to find out where he came from, Clark travels to New York to meet Dr. Swann, a brilliant scientist who holds a message for Clark from his home planet. Meanwhile Lana decides to move out of Chloe's house after the two girls get into another argument about Clark.
After a schoolmate claims to be an alien and seemingly backs it up by using heat vision, Clark investigates and begins to believe that the guy is from his planet Krypton. Meanwhile, after Helen discovers a locked room in the mansion she demands to know what is behind it, forcing Lex to come clean about his investigation of Clark.
After Lana is almost assaulted by a college student, Clark loses control and injures the boy. When the Kents are sued for punitive damages that could cost them the farm, Clark begins to question his powers while trying to find a way out of the lawsuit. Meanwhile, Helen's ex-boyfriend arrives in town intent on winning her back, but when she turns him down, he stabs her, prompting Lex to take the law into his own hands.
Clark stumbles upon a robbery of a LuthorCorp truck carrying kryptonite and is stunned to realize he can't stop the thieves because they are as strong as he is. To keep Clark from going to the police, the thugs attack Jonathan and Martha, leaving Clark feeling powerless and desperate for a way to protect his parents.
After Lana is visited by the ghost of a childhood friend, she turns to Clark for help in uncovering the truth about her new visitor. However, after Clark realizes the little girl is actually a kryptonite-enhancedclone, he rushes to save Lana before the revenge-seeking child harms her. Lex learns that Lionel is funding the krypto-cloning research.
Dr. Walden wakes up from his coma and tells Lex and Lionel that Clark is an alien and must be destroyed. Meanwhile, a romantic encounter between Clark and Lana hints at a promising future, but after Chloe finds out they are together, Lana pulls back.
A sense of foreboding surrounds Smallville as Clark must choose between staying with Lana and his family or fulfilling his destiny to rule the Earth. Meanwhile, Lex and Helen plan their upcoming wedding, but outside forces may ultimately keep them apart. Also, a hurt Chloe considers Lionel's offer to investigate Clark.
There are three weddings mentioned this season. Lex and Desirée have a beautiful reception in Heat. Lex and Helen have a church wedding in Exodus. Aunt Nell plans to marry Dean Winters, but that wedding doesn't get any screen time.
Smallville's version of comic character Jor-El is introduced.
Clark learns more about his heritage in this season. He learns that his birth name is "Kal-El" and that he's from Krypton (Rosetta). This is also the first season to use the term kryptonite in dialogue. (Visitor).