Clark is living a decadent life in Metropolis by stealing money, under the influence of the red kryptonite ring, only his chest is starting to hurt more from the scar.
Jonathan acquires superpowers courtesy of Jor-El, and he and Clark battle one another on the roof of the LexCorp. building. Meanwhile, Lex is still trying to piece together the details of his plane crash, having returned to Smallville, and figure out whether his father, or Helen, was behind it.
Clark attempts to stop a hunter from going after people affected by kryptonite rocks, but when he finds himself saving Lex from a kryptonite bullet, he ends up taking a bullet when the hunter realizes kryptonite is what makes him powerless.
Clark begins dreaming that he is being chased by a girl in need of help, but he soon learns that while the girl is real, she is neighbor who has been comatose for years. His attempts to discover the truth about the girl using Lana's assistance puts Lana in harm's way. Meanwhile, Lionel still won't commit to hiring Lex, so he requires that his son undergo complete psychological testing first.
Former star journalist Perry White comes to Smallville looking for alien stories for a tabloid television show. When he is rescued by Clark after a drunken auto mishap, he begins to suspect Clark has superpowers and sets out to expose him. Meanwhile, Lex finds out that Perry, whose career was once damaged by Lionel Luther, may hold some information about his father's past criminal acts.
After learning that Jor-El came to Earth forty years ago, he learns that Lana has suspicions about the murder of her great aunt at her great uncle's hands. Looking at a picture of the man she believes to be the true killer, Clark believes the man to be Jor-El, and further research leads him to a medallion from Krypton which allows him to see the past.
When Lana starts dating a strange new boy, she suddenly appears to be acting wildly and ends up in jail. Clark's suspicions about her boyfriend's influence lead him to learn more about him, at which time he finds out the boy has magnetic powers which can move objects and control emotions. Meanwhile, Lex tries to persuade Chloe to help him bring down his father when he learns she's already been investigating Lionel's shady history.
Lex is the target of an assassin after he visits Morgan Edge and manages to pry the truth out of him about dealing with Lionel. After he arrives at the Kent farm, alive but somewhat scathed, Clark looks for the assassin at Lex's mansion. Finding no evidence, he begins to think Lex may be losing a grip on reality, a point reinforced when his father has pronounced it so and wants Lex committed to an institution.
Lionel arranges for Lex to undergo electroshock therapy, for his son's own good, in order to wipe out his memory. Three old nemeses of Clark's try to exploit Lex's condition to entice Clark to the hospital, where they hope to ambush him and steal his powers with the aid of kryptonite. Lana, meanwhile, has an odd encounter while at the hospital.
In the midst of a jewelry shop robbery, Clark's attempt at heroism using heat vision gets refracted through kryptonite and temporarily blinds him. He quickly realizes, however, that in its place he's developed a powerful, and unwieldy, gift of super hearing.
Clark and Lana receive an e-mail from a mysterious corporation which causes them to make attempts on Chloe's life. She soon discovers that the corporation is engaging in mind-manipulation experiments and may go to lengths to keep her from reporting about them. Meanwhile, Adam moves into the apartment just above the cafe, even though Lana is wary of his secretive nature.
Clark's classmate Jordan has the power to see ahead in time, and Clark learns, to his horror, that Lana's near future supposedly involves a tragic, fiery death. Meanwhile, Chloe continues to do more investigative snooping to discover the truth about Adam.
Clark must help protect Pete when Pete is under the threat of a bunch of racing thugs for intentionally throwing a street race. Meanwhile, Jonathan's bargain with Jor-El begins to unravel.
When Clark must use his powers in the presence of a new classmate, Alicia, the two end up getting close when he learns that she also has secret powers she must keep hidden. Their relationship ends up becoming a little too close for Clark's liking when she refuses to let him spend time with anyone else, especially Lana. Lana, meanwhile, turns to Lex for some more effective probing into Adam's life.
Jonathan goes in for bypass surgery, and while in the waiting room, Clark meets a young man named Garrett whose brother died as a result of liver failure.
Clark has a premonition of tomorrow when Lana's desperate call for help from the forthcoming day reaches him in the present. Discovering Lana to be alive, he realizes that Adam is going to kill her when he hears the sound of gunfire before the call is cut off. After Lex and Clark go to the labs at Luthercorp where Adam was being held, Lex discovers a strew of dead employees' bodies and suspects that his father is up to something.
Jonathan's odd behavior and detachment from Clark and Martha makes Clark think Jor-El may be trying to communicate a message using the key. After returning to the hidden cave to communicate with Jor-El about his intentions, he is discovered by Lionel Luthor who, suspicious of Clark's identity, then goes to see Dr. Swann.
When Chloe inhales a gas derived from Kryptonite, she finds that contact with people causes them to be completely honest in what they say, and decides to use the power of her newfound truth-inducer to get the truth about Clark out of Jonathan and Martha. Clark must intervene and figure out how to save Chloe and preserve his secret when the effects of the gas become potentially fatal for her.
Lex decides to join forces with Dr Garner, whom he believes can help him bring Lionel to justice by reinstating the memories of his father's shady history. Clark fears this will also make Lex learn the truth about his powers, but when he tries to stop Lex, he runs into Lionel, who then subjects him to the same treatment as Lex in order to find out about Clark for himself.
A Kiwatche Indian takes a knife from the secret cave, and soon is endowed with the same gifts as Clark, leading him to believe is a powerful figure from Indian lore named Naman sent from the stars. Clark soon fears that based on the lore, the man may turn the blade on Lionel Luthor.
Clark makes the decision to open up to Lana about his powers and his true origins so they can be with another. Meanwhile, Lex learns he'll go to prison if he doesn't deliver incriminating knowledge about Lionel to the FBI within 24 hours, while an FBI agent takes Sam hostage and begins to use methods of torture to coax the truth about Clark out of him; and, Lois recognizes Wes the Super Soldier b
When an attractive stranger named Kara shows up at Clark's doorstep, one who has powers of her own and claims to hail from Krypton, she tries to steer him toward his true purpose and coerce Jonathan into telling him about his secret bargain with Jor-El. Meanwhile, Clark's relationships with Lana and Lex take two different, but equally devestating turns, and Lex assists the FBI in its probe of Lionel.