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Clark rescues his telepathic friend Ryan from a doctor intent on keeping him for experimentation and to harness his powers.

When Lionel Luthor is shot, several people are suspected, the main suspect being Jonathan.

Clark learns more secrets from his past when a woman shows up claiming to be his mother.

When a college student gets rough with Lana, Clark loses control and injures the boy, leading to a lawsuit and causing him to reevaluate the potency of those powers. Meanwhile, Lex goes outside the law to hunt down Helen's ex-boyfriend turned stalker, after she is nearly murdered following her refusal to reunite.

Calling (Part 1)
Dr. Walden awakens from his coma and escapes to the cave which provides him with the answers regarding Clark's alien origins. When he subsequently warns Lex and Lionel Luthor and advocates that they kill him, Lionel offers Chloe a Daily Planet job in return for an investigation of Clark. Meanwhile, Clark worries that a kiss shared with Lana has created tensions within their friendship with Chloe.

Whitney returns from the Marines intent on reigniting old romances with Lana, but Clark, suspicious of those intentions, discovers that Whitney is actually shapeshifter Tina Greer, who has returned to get Lana.

Hoping to learn about his true origins, Clark goes to New York to meet a scientist who has a message for him from his home planet. Meanwhile, Lana moves out of Chloe's house following a spat over Clark.

Exodus (Part 2)
Clark must choose between his love of Lana and his family and fulfilling his destiny to preside over Earth. When he accepts his preordanied fate, he visits the spaceship at sunset which imprints the ancestral mark upon his chest. Lex and Helen plan their upcoming wedding, but outside circumstances threaten to keep them from being together. Meanwhile, Chloe, still stinging from Clark's decision to be with Lana, takes up Lionel Luthor's offer to help him investigate Clark. Clark attempts to destroy the spaceship, and the resulting blast causes Martha to lose her baby in a car accident and Clark, donning a kryptonite ring, to leave town out of guilt.

Lex finds his long-lost brother, Lucas, whom Lionel gave up for adoption, and brings him back to Smallville.

Vortex (Part 2)
Clark's secret identity is threatened when he saves Lana from the middle of a deadly tornado. The storm traps Mr. Kent and the reporter and the two bond as they try to escape. But when the storm clears, the reporter once again turns on the Kents until Lex steps in and kills him.

Clark falls into a cave where he meets a beautiful girl and her grandfather and finds ancient drawings on the wall that may have prophesized his arrival.

A mysterious stranger leaves notes for Lana at her parents' graves. Despite Clark's advice to ignore the notes, Lana follows the stranger home to find that his parents keep him locked in chains. But when Lana and Clark free the boy, they soon find that he was chained up for a reason.

A high school swimmer suddenly dies of old age and Chloe uncovers a deeper mystery when the swimmer's girlfriend is suspected of stealing his life force as well as a long line of victims. Clark forces his father and grandfather back together after a long term feud. And Lana discovers a picture that indicates her mother had an affair with a man who might be her true biological father.

A shard of red kryptonite in Clark's class ring causes him to go wild and to lose all his inhibitions.

Pete finds Clark's spaceship in a cornfield when he comes to the aid of a hit-and-run victim. Clark is forced to reveal the truth about his background.

When Lana is haunted by the ghost of a childhood friend who drowned at age 10, Clark helps her unravel the mystery and they learn the ghost is a clone of the girl and uncover a cloning lab which uses kryptonite to age the clones. After the lab is later mysteriously cleaned out, the trail leads to Lionel Luthor.

Clark witnesses a student start a fire with his eyes after being bullied by a gang, after which time he and Chloe investigate the student's claim that he is an alien.

A parasite transforms Chloe and Pete into daredevil personalities, and Pete coaxes Clark into accompanying them on a dangerous activity after exposing him to red kryptonite.

Lex hires a team of thieves to infiltrate his father's office after learning of a surveillance on him, only the thugs take Lionel and Martha hostage, leaving Clark to rescue them while keeping his powers a secret.

A sexy new teacher uses her power of pheremones to get Lex to marry her. Clark's new power of heat vision is more than he can control.

Clark has suspicions about a boy who begins dating both Lana and Chloe and tries to warn them, especially after discovering that he can split into two separate versions of himself.

While burying the ship key, Martha becomes ill from irradiated-meteor spores, and it is soon discovered that she is pregnant with a son. Clark also becomes ill from the spores when he tries to hide the ship during a DCA visit. After stealing the key back from the DCA base, Jonathan rushes Clark to the hospital, where Doctor Bryce has some questions for Jonathan about Clark and Martha's condition and learns of Clark's true nature from a blood sample.

Clark finds himself overpowered by some thugs who robbed a LuthorCorp truck full of kryptonite to turn it into a performance enhancing drug, one of which is a Smallville High star baseball player. He is powerless to protect his parents when the thugs attack them to prevent him from going to the police so he must get creative with some help from Lex.

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