Under the influence of red kryptonite, Clark is following a life of crime in Metropolis while his friends and parents desperately try to find him. Lex is forced to confront his personal demons on a desert island, while Lionel holds a funeral for his presumed-dead son. And Jonathan Kent must pay a high price for the power necessary to bring his son back home.
Clark gives up the ring and its effects rather than hug his father, and both he and the rescued Lex return to Smallville. Clark must deal with crime lord Morgan Edge, who has followed him to Smallville, while Lex must determine who tried to have him killed - Lionel or Helen.
Clark discovers someone is hunting people affected by the kryptonite rocks and the hugger's next target is Lex. Clark uses his powers to save Lex, but is caught off guard when the hugger learns his weakness and shoots him with a kryptonite bullet.
Clark is being pursued by a frightened young girl who needs his help. However, after he discovers she is actually a comatose neighbor who should have woken up years ago, he enlists Lana's help to uncover the truth which puts Lana in grave danger. Meanwhile, Lionel demands that Lex undergo a full psychological evaluation before he hires him.
Perry White, a once promising journalist whose career was destroyed by Lionel Luthor, arrives in Smallville in search of alien stories for a tabloid news show. In spite of being constantly inebriated, Perry believes he has witnessed Clark using his extraordinary speed, so he devises a dangerous scheme to expose Clark's superpowers. Meanwhile, Lex learns that Perry has powerful incriminating evidence of Lionel's shady past.
Clark discovers that Jor-El was on Earth forty years ago. Lana's great uncle, who was convicted of murdering his wife forty years ago, shows her a picture of the man he believes really killed her aunt, and she is shocked to discover the drifter looks just like Clark. Sure that the man is Jor-El, Clark's investigation leads him to a kryptonian medallion that allows him to see bits of the past and the life that Jor-El started for him long before he arrived on Earth.
Clark is suspicious when Lana suddenly becomes attracted to a fellow student and begins to act rebelliously, which eventually lands her in jail. Clark's suspicions are confirmed when he discovers Lana's new boyfriend has magnetic powers that can move objects and alter human emotions, but when he tries to free Lana from the paranormal hold that is controlling her, she tries to hug him. Meanwhile, Lex discovers Chloe has been delving into Lionel's past and tries to get her to join forces against his dad.
Lex locates Morgan Edge and gets him to admit to dirty dealings with Lionel, but before Lex can take it to the authorities, someone tries to hug him at the mansion. Barely surviving, Lex flees and asks Clark for help. However, when Clark returns to the mansion to investigate he finds nothing amiss, and begins to wonder if it really happened, especially after Lionel announces Lex has had a psychotic break and must be institutionalized.
Three of Clark's former opponents approach Lex to enlist his help in luring Clark to the hospital after they hear that Lionel has requested Lex be given electroshock therapy to erase his memory. However, the plan goes awry when the villains double-cross Lex and use kryptonite to steal Clark's powers. Meanwhile, Lana meets a mysterious stranger in the hospital.
Attempting to stop a robbery, Clark is temporarily blinded when he shoots off a burst of heat vision that is accidentally reflected back into his eyes by a piece of kryptonite and soon realizes his body has developed super-hearing to compensate for his lack of sight. However, as it was in the beginning with his other gifts, Clark doesn't quite have his new power under control.
Clark and Lana each make an attempt on Chloe's life for unknown reasons after they receive a mysterious e-mail from the Summerholt Institute. Clark must discover the source of these e-mails after Chloe reveals she has uncovered proof that they are doing mind-control research at the lab and realizes they must be trying to hug her in order to prevent her from writing an expose. Meanwhile, Lana decides to rent the apartment above the caf to Adam even though she feels he is hiding something dangerous about his past.
Clark discovers that his schoolmate Jordan can foresee the future, but is horrified when Jordan tells him he "sees" Lana dying in a fire in the next few days. Meanwhile, suspicious of his behavior, Chloe investigates Adam's background and discovers some disturbing news.
After Pete refuses to throw a street race, the thugs that run it threaten his life, so he asks Clark to use his powers to stop them. Furious that Pete would put himself in this position, Clark must figure out a way to save Pete and still protect his secret. Meanwhile, Jonathan begins to suffer the consequences of his deal with Jor-El.
Clark is forced to use his powers in front of Alicia, a new girl at school, but he is surprised to find out she has powers of her own. The two develop a bond through their shared secret, but things turn ugly after Alicia becomes obsessive about sharing Clark with anyone else especially Lana. Meanwhile, Lana asks Lex to investigate Adam.
While his father is awaiting surgery, Clark befriends a young boy, Garrett whose brother Vince just died from liver failure. However, everyone is shocked when Vince shows up alive and seemingly well - until his liver starts failing again. In a desperate attempt to keep his brother alive, Garrett straps a Kryptonite bomb to himself and demands that Vince be given Jonathan's liver or he will blow up the building.
Clark receives a panicked call from Lana and hears a gunshot before the line goes dead, but when he arrives at the Talon he is stunned to discover she is alive and well. Clark realizes the phone call came from the next day and that Adam is the one who will shoot Lana.
When Jonathan begins to act strangely, Clark believes Jor-El is sending Jonathan messages through the key and is the cause for his father's withdrawal from the family. Clark goes down to the caves to confront his biological father but Lionel catches him there and begins putting the pieces together leading him straight to Dr. Swann. As the two billionaires face off, a deal is struck and Lionel's true motives are revealed.
When Chloe accidentally inhales a mysterious krypto-gas, she discovers it acts as a truth serum to anyone who comes in contact with her and decides to take advantage of her new power by going to the Kents to find out Clark's secret. However, her new power comes with fatal consequences and Clark must find an antidote before she discovers the truth about him or worse, dies.
Believing that key information about his father's past was lost when his memory was erased, Lex decides to join an experimental program with Dr. Garner to regain the information so he can turn his father over to the FBI. Knowing that Lex will discover his secret if he regains his memory, Clark tries to stop him but is caught by Lionel and the doctor and exposed to the same radical treatment so that Lionel can solve the mystery of Clark's past.
Jeremiah Holdsclaw, a young Kiwatche Indian, steals a mythic knife from the tribal caves and gets superpowers similar to Clark's. Jeremiah believes he is the fulfillment of the ancient prophecy of Naman, "the man who fell from the stars." He sets out to hug Lionel with the knife, and Clark must stop him without revealing his own secret.
Clark decides to tell Lana his secret so they can finally be together. Meanwhile, an errant FBI agent kidnaps and tortures Pete to try and force him to reveal Clark's secret. Also, Lex panics after the FBI gives him 24 hours to turn over information on his father or face jail time, but help arrives from an unexpected source.
Kara, a beautiful superpowered girl from Krypton, entices Clark to join with his father and embrace his destiny. Clark is left without support after Pete's departure when Jonathan reveals the deal he made with Jor-El. At the same time, Clark's relationships with Lex and Lana take unexpected turns, leaving him with no one but Kara to turn to.