Pete finds Clark's spaceship, forcing Clark to reveal his secret to his best friend. Dr. Hamilton is plagued by kryptonite-fueled illness and focuses on Pete. Meanwhile, Lana has to deal with Nell and her plans to remarry while Lex and Lionel adjust to life together.

Whitney returns to Smallville, eager to start back up where he left off with Lana. But everything isn't what it seems...

Students are engaging in wild, sometimes suicidal stunts, and Chloe and Pete are the next ones to become "infected."..and they use a piece of red meteor rock to get Clark to join them.

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.

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.

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.

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 is drawn to the state penitentery by one of the kryptonian crystals, which Lionel is using to switch bodies with Lex. Clark intervenes and Lionel enters his body instead. While Lionel uses his newfound super-powers to regain his lost fortune and alienate Clark's friend, Clark must convince his parents that he is the "real" Clark and reverse the processs, while avoiding murderous convicts.

Clark is approached by Met U for recruitment and meets Geoff, a former Smallville resident. It soon becomes apparent that he is using his powers to paralyze anybody who gets in his way...including Lois.

After a nightmare, Clark goes to the cave to confront his father Jor-El. Jor-El warns that the crystals have fallen into human hands and have triggered a new meteor shower which will annihilate the Earth unless he reunites the three crystals. Meanwhile, Lex helps Lana, who has apparently commited murder, but then turns against her to get possession of her Kryptonian stone. As disaster looms, Chloe and Lois try to find Lana while Clark attempts to reassemble the stones, and Jason returns to make things unpleasant for the Kents.

Having been transported to the Fortress of Solitude, Clark is confronted by Jor-El, who tells him he cannot return to Smallville, instead he must stay and prepare to save the planet. Also, transported to the Fortress, Chloe is unable to handle the sub-zero temperature and collapses, begging Clark to use his powers to save her. Jor-El forbids him to leave, but finally acquiesces, telling Clark he must return before sunset or there will be dire consequences. Meanwhile, Lana is horrified when she sees two Kryptonian aliens emerge from a spaceship discovered in the remnants of the meteor shower. The two aliens destroy what's left of the town searching for Kal-El.

At a party at Crater Lake, Lois is saved from drowning by Arthur "A.C." Curry. Arthur has incredible swimming abilities, but also a secret agenda aimed at...Lex. Meanwhile, Professor Fine discussed Lex's weapons-manfucturing operations with Clark.

When Martha comes down with a strange disease, Professor Fine convinces Clark that Jor-El is responsible and that the Fortress must be trying to eliminate the father of Kal-El. But Professor Fine has an ulterior motive which comes to fruition when they arrive.

Clark is hypnotized by a woman who uses a supposedly magical charm to control others - he reveals his super powers and is sent to kill Lex. Meanwhile, Lex has tracked down the missing Professor Fine and plans to confront him, unaware that Clark is coming to murder him.

Clark befriends a little girl who has the ability to telekinetically shatter glass, then comes to her aid when it's believed she killed her mother in a brutal stabbing attack. Meanwhile Lex and Lana grow closer together and Chloe finds out about it.

In the aftermath of Zod's activities, Clark develops a new power. Lois gets a new job, Lana takes a new step in her relationship with Lex, and Lex has to deal with a new danger. Meanwhile, an old friend of Lex's arrives in Metropolis.

After being shot while stopping a carjacking, the Green Arrow begins acting strangely. Chloe and Clark investigate and find Oliver is taking a super drug that while healing his wound, has some dangerous side effects.

A boy named Tobias was blinded by the meteor shower but given the ability to identify other meteor freaks. Lex is using Tobias to locate other people with abilities so that he can perform experiments on them. Lana learns of Tobias and is fearful that he will name Clark as a freak, so she offers him a cornea transplant to keep him quiet. But Tobias has some surprising news.

Clark discovers the reason Lana married Lex then and sets out to kill Lionel. Lex tries to use DNA from the last phantom to power his super-soldiers. Lois goes to a dam to search for Lex's lab but is caught by a security guard and fatally injured. Chloe's power is discovered.

Clark and Lois meet Smallville's newest arrival face-to-face, and she has some surprising news. Clark decides to leave Smallville and continue with his superhero training but Jor-el informs him that a new Kryptonian menace has arisen.

Clark hears his mother's voice trapped in Kara's crystal, and releases her. She gives him Jor-El's ring made of Blue Kryptonite, which strips him of his powers.

Jimmy catches a red and blue blur on film when he takes a picture of Clark saving Lois from a mugger; after Tess decides to run the picture on the front page of the Daily Planet, Clark fears his identity will be discovered.

Clark discovers that Lana is missing; Tess reveals what really happened to Lana when she woke up from her Brainiac-induced coma; Tess is shocked by what she discovers in a secret LuthorCorp facility.