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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.
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Clark gives up the ring and its effects rather then kill 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.
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Clark discovers someone is hunting people affected by the kryptonite rocks and the killer's next target is Lex. Clark uses his powers to save Lex, but is caught off guard when the killer learns his weakness and shoots him with a kryptonite bullet.
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Clark dreams he 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.
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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.
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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.
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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 kill him. Meanwhile, Lex discovers Chloe has been delving into Lionel's past and tries to get her to join forces against his dad.
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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 kill 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.
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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.
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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.