Clark rescues Lana from the giant tornado and takes her to the hospital. When he returns home, Clark learns the ship is gone, and that his father chased Roger Nixon into the storm. Lex is wracked with guilt over not helping his father sooner, who is now in the hospital, and makes a decision that costs his father his eyesight. Jonathan and Nixon attempt to dig themselves out of the crypt they fell into after a mobile home dropped out of the sky on top of them. Clark shows up before the two men lose all oxygen, but the meteor rocks weaken him. Nixon takes advantage of the situation, and kidnaps Clark. Lex shows up and saves Jonathan's life by shooting Nixon before he can kill Jonathan.

During a record heat wave, Clark develops a new ability, heat vision, which causes him to have uncontrollable bursts of heat from his eyes. Lex marries Desiree Atkins, a woman he barely knows, who it turns out is able to control men with meteor rock-enhanced pheromones. With Jonathan's help, Clark discovers the trigger for his heat vision and learns to control his new ability. Desiree attempts to use her pheromones on Clark, but he is resistent. Instead, she convinces Jonathan to kill Lex, so that she can inherit his fortune. Clark manages to save Lex before either Jonathan or Desiree can kill him.

After Pete discovers the spaceship in a cornfield, Clark goes against his parents' wishes and reveals his secret to Pete. Pete's reaction makes Clark begin to regret his decision. Dr. Hamilton, suffering from overexposure to the meteor rocks and exhibiting the same tremors as Earl Jenkins, steals Clark's ship. When Lex refuses to believe his rants about a ship, Dr. Hamilton seeks support from Lionel Luthor. Pete's loyalty is tested when Dr. Hamilton kidnaps him in an effort to find out how to open the ship. Clark arrives, but Hamilton's overexposure to the meteor rocks sends him into deadly convulsions.

Clark goes against his father's wishes and purchases an expensive high school ring. The ring contains red meteor rock, and affects Clark mentally. With his inhibition gone, Clark begins to act out of character. He ruins a date with Lana when he starts a fight in a bar. Showing resentment toward his parents for forcing him to live the life of a farm boy, Clark decides to use his abilities to become rich and leave Smallville. It takes both Pete and Jonathan, working together, to stop Clark and remove the ring from his hand. Clark tries to apologize to his parents, but Jonathan suspects that Clark was expressing his true feelings. Lana refuses to accept Clark's apology when he cannot explain his actions to her.

When a student is pulled out of the school pool, having aged 60 years in a few seconds, Clark and Chloe decide to investigate. They discover an 80 year trail of similar events left behind by Chrissy "Missy" Parker, another student. Lana discovers a photo of her mother with an unidentified man. Learning that her parents were separated for a short time, she believes the unidentified man may be her biological father. Without a fresh victim, Missy's body begins to age rapidly. Clark manages to keep her from killing the new principal, which causes Missy to deteriorate into dust.

A woman named Rachel Dunleavy shows up claiming to be Clark's biological mother. Dunleavy kidnaps Lex and threatens to kill him if Lionel doesn't reveal the truth about Clark's adoption. Lana finds her biological father, Henry Small, and confronts him, only to find out that he is not interested in her. Jonathan reveals to Clark that he made a deal with Lionel Luthor, in an effort to make sure he and Martha could adopt Clark, which enabled Lionel to buy the Ross Creamed Corn factory. Rachel witnesses Clark using his abilities and realizes that he isn't her son. Lionel admits to Lex that he did father another child, but that it died as an infant.

After his aunt abandons him, because of money problems, Ryan phones Clark for help. Clark rescues Ryan from the Summerholt facility, where the boy was being held an unwilling subject of experimentation, and brings him back to Smallville. He soon finds out that Ryan has a tumor in his brain, and that he only has a couple days left to live.

Ian, a straight-A student, has the ability to duplicate himself. He uses his power to take extra classes, and date both Lana and Chloe at the same time. Clark and Pete reveal Ian's secret, which forces Ian to try and kill both of the girls. Meanwhile, Lex attends an anger management session, where he meets Dr. Helen Bryce.

2.10 Skinwalkers

Clark stumbles into a local Native American cave, located below a new LuthorCorp construction site, and discovers symbols in an alien language on the cave walls. A local Native American, Joseph Willowbrook, and his grand-daughter Kyla, recount a story that reflects Clark's life. In an effort to save the land, Kyla tries to scare the Luthors away, using her ability of skinwalking, but she is mortally injured during her attack on Lionel.

Whitney Fordman returns from overseas, to everybody's surprise. Claiming to have lost some of his memory during battle, he tries to get back together with Lana, ignorant of the Dear John letter she sent. Not wanting to hurt him, Lana submits to his attempts to win her back, but Clark discovers that Whitney is actually Tina Greer. When Clark confronts Tina, she immobolizes him using green meteor rock. Left helpless in the Kents' storm cellar, Clark is saved by his spaceship. During a later confrontation with Clark, Tina injures herself and dies

After Lex is defeated in a takeover bid by Lionel, he discovers that his mansion is full of listening devices. Lex starts a plan to bug LuthorCorp's headquarters, but aborts when he finds out that Martha and Lionel are headed there. The abort is botched when the workers want to steal from the LuthorCorp vault. While held hostage, Martha learns that Lionel has files on Clark, and bars of refined meteor rock.

2.13 Suspect

Lionel is mysteriously shot at the Luthor mansion, leaving behind a huge list of suspects with various motives to want him dead. Jonathan, who is found unconscious in his truck with a bottle of vodka and a gun in his hand, is arrested as the prime suspect. Clark and Pete investigate, and discover an elaborate plan orchestrated by Sheriff Ethan.

Pete and Chloe are infected by bug-like creatures that burrow into the necks of those who get close enough. The bugs cause people to engage in extremely risky behavior. Pete uses red meteor rock to get Clark to join them. The red meteor rock is incidentally removed, and Clark manages to get both his friends to the hospital. Lex hires Dr. Frederick Walden, an expert in ancient glyphs, to try to translate the language found on walls of the Kawatche Caves.

2.15 Prodigal

Lex discovers that his brother, Lucas, is still alive. Lionel has been looking after Lucas, and uses him to steal away Lex's inheritance, so he cannot buy-out LuthorCorp. Penniless, Lex moves in with the Kents. Lucas, dissatisfied with Lionel's plans for him, discovers that Lionel has been faking blindness for a while. An elaborate scheme with Lex reveals Lionel's lie, and Lex secures his inheritance back into place.

 

Martha, who has been hiding the key to the spaceship, becomes extremely sick from inhaling dust of green meteor rock that was underground. The Kent farm is quarantined, and the key discovered. Clark, who inhaled the meteor dust as well, falls sick too. After testing his blood, Dr. Helen Bryce realizes that Clark is different. Martha is revealed to be pregnant after the ship removes her poisoning.

Clark decides to place the key into a slot in the cave wall. Upon inserting the key, the wall downloads him with the language of the cave. Dr. Walden discovers the key and uses it himself, but the information overload puts him in a coma. At home, Clark's heat vision forces him to etch a symbol onto the barn door. He is contacted by Dr. Virgil Swann, who educates Clark about Krypton, his home planet. Using the key on the ship, he uncovers a hidden message from his biological father stating that his destiny is to conquer Earth.

After Lana is assaulted by a college student, Andy Conners, Clark loses control and seemingly injures the boy. When the Kents are sued for punitive damages, 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. When she turns him down, he stabs her, prompting Lex to take the law into his own hands.

 

A group of thieves hijack a LuthorCorp van, and steal a shipment of refined green meteor rock. Clark stumbles upon the robbery, but is no match for them. It turns out that they are manufacturing and inhaling liquid kryptonite, which leads to enhanced strength. Lionel offers to fund the Torch and a position at the Daily Planet, if Chloe does an investigative report on Clark

Lana thinks she is seeing ghosts, when an old childhood friend, Emily, who died six years prior, appears. Clark discovers that the child is indeed real. By moving extremely fast, the girl seems to disappear and walk through walls. Clark learns that Emily's father has been cloning her, with the help of green meteor rock. The flaw with the Emily clone is that she has no sense of morality, which eventually puts Lana in danger. Meanwhile, Lex prepares for his wedding with Helen.

Dr. Walden wakes up from his coma, and tells Lex and Lionel that Clark is an alien that must be destroyed. A romantic encounter between Clark and Lana is quickly dismissed when Chloe finds out they are together. During a rehearsal for Lex and Helen's wedding, Clark hears a strange voice calling from the storm cellar.

The will of Clark's biological father, Jor-El, informs Clark he must leave Smallville. Not wanting to leave his family and friends, Clark steals Lionel's copy of the spaceship key made out of refined green meteor rock and sticks it into the ship, destroying it. The blast from the explosion causes Martha to lose her baby. Grief stricken, Clark decides to leave Smallville. During his honeymoon flight, Lex wakes to find the plane going down and Helen and the pilot missing.