Clark saves Lana from the tornado, leading Lana to be suspicious of Clark. While protecting Clark's secret, Jonathan gets trapped with reporter Roger Nixon in an underground mausoleum. Lex and Clark search for Jonathan.

On the first day of sophomore year at Smallville High, Clark develops a new superpower: heat vision. Desiree Atkins, the new Biology teacher, uses Kryptonite-enhanced pheromones to get Lex to marry her and then attempts to seduce Clark.

After Clark's friend Pete discovers Clark's 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.

After Clark buys an expensive class ring made from Red Kryptonite, he immediately begins acting very out of character and starts abusing his powers. Meanwhile, Lex struggles to adjust to Lionel moving into the Luthor Mansion.

Lana starts receiving romantic love notes from a boy called Byron Moore, who is being imprisoned in his basement by his parents. Meanwhile, Lionel hires Clark's mother as his personal assistant.

When the farm runs into financial troubles, Martha calls her estranged father for help. Meanwhile students at Smallville High are mysteriously aging rapidly and the school's new principal takes issue with Clark's close friendship with Lex.

A woman appears in Smallville claiming that Clark is her biological son by Lionel Luthor, and she kidnaps Lex to force a confession from Lionel. Clark demands that his parents explain what role Lionel Luthor played in his adoption.

Clark rescues mind-reading Ryan James from a research hospital that treats him like a lab rat. Ryan's guardian doctor sues to get Ryan back, and Clark learns that Ryan has a brain tumor that needs treatment.

Smallville High student Ian Randall uses his self-cloning ability to secretly date both Chloe and Lana. Meanwhile, Lex attends anger management classes where he becomes intrigued by an attractive local doctor, Helen Bryce.

Clark falls into an underground cave system where Native American teen Kyla Willowbrook is researching her ancestor's cave paintings and believes Clark may be the answer, while her grandfather attempts to save the caves from LuthorCorp.

Whitney Fordman returns to Smallville unannounced and receives a hero's welcome from all but Clark who fears his return will put strain on his relationship with Lana. However, all is not as it seems as Whitney begins behaving erratically.

When Lex discovers that his father had surveillance devices planted in the mansion, he hires a group of criminals to do the same to LuthorCorp Plaza in Metropolis, unwittingly putting both Lionel and Martha's lives in danger.

Lionel Luthor is shot by an unknown assailant, leading Sheriff Ethan to suspect a drunken Jonathan Kent. As he attempts to prove his father's innocence, Clark learns that Lex and Dominic Senatori have their own motives for killing Lionel.

After attending an unauthorized rave in the caves underneath Smallville, Pete and Chloe become infected with a parasite which turns them into adrenaline junkies, threatening to expose Clark's secret and ruin his date with Lana.

Lex locates his long lost half-brother Lucas in Edge City and takes him back to Smallville as part of his plan to overthrow their father Lionel. However, Lex faces betrayal when Lucas decides to side with Lionel instead.

Attempting to hide the key to Clark's ship in the farm's storm cellar, Martha unknowingly breathes in toxic meteor rock spores and falls ill. To make matters worse, the Disease Control Agency wish to conduct a full search of the farm.

When Clark feels compelled to insert the ship's key into the slot on the cave wall, he is suddenly able to understand the cave's strange symbols and is contacted by Dr. Virgil Swann who may hold the answers he seeks about his home planet.

Clark saves Lana from a group of drunken customers at The Talon but faces scrutiny from Smallville's strict new Sheriff Nancy Adams. Lex becomes concerned when Helen's obsessive ex-boyfriend arrives in Smallville and begins following her.

Following an argument with Chloe, Clark witnesses a Smallville High student rob a LuthorCorp van transporting kryptonite. Avoiding police questioning, Clark takes matters into his own hands but unwittingly puts his family in danger.

Lana is terrified when she is seemingly visited by the ghost of her deceased childhood friend Emily. As Clark and Lana investigate, they find there may be more to Emily than meets the eye and that Lionel Luthor may have some involvement.

As Lex and Helen prepare for their imminent wedding, Clark and Lana navigate their blossoming romance. Meanwhile, linguist Dr. Walden awakens from his coma and sets out to kill Clark Kent, believing him to be a threat to mankind.

Clark is contacted by his biological father Jor-El who tells him he must leave Smallville to fulfill his destiny, just as everything is going right for him. Torn between his heritage and his upbringing, Clark must make a difficult choice.