Ian Randall is a mentally unbalanced, overachieving student desperate to succeed who gets a 'C' from his stern shop teacher John Frankle. Ian freaks out, duplicates himself and kills Mr. Frankle. The meteor-rock mutant simultaneously invites Lana and Chloe on a literal 'double date', aiming to get a scholarship from Luthor Corp to Yale by using the girls who know Lex Luther. Meanwhile, Lana moves to Chloe's house to live with her and divorced father after Nell leaves town. Clark tries to advise Lana and Chloe about the personality and ability of Ian, but he is misunderstood. Elsewhere, Jonathan breaks his leg, and Lex Luthor meets Dr. Helen Bryce, who is treating Jonathan where an immediate attraction develops between Lex and Dr. Bryce.

Just as Clark and Lana are making progress and he finally sums up enough courage to ask Lana out on a date to a local festival, an old flame rekindles when Lana's former beau, Whitney Fordman, returns from the Marines to make up for lost time. But something is wrong with Whitney for he isn't himself, and Clark sets off to find out what's wrong and why Whitney doesn't remember some things. But the big twist is that the real Whitney was killed in action in Indonesia, and that the meteor-rock shape shifter Tina Greer (from the 'X-Ray' episode) is impersonating Whitney to get romantically close to Lana. Soon, Clark finds himself in a bind then Tina traps and immobilizes Clark in his storm cellar tied up with Lana's kryptonite necklace, until help comes from of all things... the spaceship. Meanwhile, Lex confronts Helen Bryce about her employment with Lionel and questions her motives for being in Smallville.

While hiding the spaceship key in the farm's storm cellar, Martha Kent breathes some unknown meteor-rock spores and immediately gets ill. She is sent to Smallville Medical Center under the care of Dr. Helen Bryce, and the results of her blood tests are sent to the Disease Control Agency (DCA). Because DCA agents are coming to inspect the farm and put it under quarantine, Clark and Pete hurry to move the spaceship. Clark inhales some of the spores and also gets sick, weakening him. The DCA agents find the key, so Jonathan Kent must retrieve it from a military base, expecting a miracle to save the lives of Martha and Clark. With Clark having lost his powers, Helen takes a sample of his blood for examination, and begins to suspect Clark's secret. Meanwhile, Lex fears losing Helen when she gets an offer to leave Smallville to study medicine at a prestigious hospital on the East Coast. Lex also finds out about Clark's condition and secretly takes Helen's medical file on him.

When the weird and lonely teenager with healing power Cyrus Krupp claims to be an alien, Clark approaches to him trying to know his origins to determine if Cyrus is a Kryptonian alien, or if he's just a crazy meteor-rock mutant who thinks he's an alien. Meanwhile, Dr. Helen Bryce moves to Lex's mansion, but she realizes that her skeleton key opens all but one room. Lex eventually shows her the inside of the room to reveal his study work about the meteor shower, and about Clark Kent. Also, Lana asks Clark to help her look after her sick prized horse which Cyrus heals the animal. He also continues to claim that his biological parents are coming to take him away.

When Lana is assaulted by three drunken customers at The Talon, Clark defends her and ends up throwing the main antagonist onto the new Sheriff's car. The new uptight Smallville sheriff, Nancy Adams, arrests Clark for assault and battery but later dismisses the charges and gives Clark 40 hours of community service instead. Andrew Connors, the man that Clark threw onto the Sheriff's car, fakes a serious injury and attempts to sue the Kents. With the abrasive Sheriff Adams unwilling to help Clark and his family, Lana decides to help Clark expose Connors as a phony. Meanwhile, Helen is stalked by her ex-boyfriend, Paul Hayden. When Paul attacks and nearly kills Helen, a vengeful Lex teams up with Clark to track down Paul to the train station before he can skip town.

As Clark and Lana get more romantically close to each other, the comatose Dr. Fredrick Walden recovers and repeats the sentence "the day is coming, and he will rule the world" many times. He believes that Clark Kent is a menace to mankind. He escapes from the mental institution using a strong power he has achieved and tries to eliminate Clark. Meanwhile, Dr. Helen Bryce returns to Smallville for her engagement party with Lex Luthor, and finds her office broke in and the blood sample of Clark Kent stolen. But who took the blood sample and her office files? Lionel or Lex? Clark is asked by Lex to be the best best man, and Martha and Jonathan Kent to replace his missing parents, as Clark begins hearing voices coming from his spaceship. Also, the evil Lionel Luthor continues playing mind games by trying to poison the relationship of Helen and Lex, as well as Chloe and Clark by offering her an intern job in Metropolis in exchange for her to investigate Clark. But unfortunately, Lionel overhears the revelations of Dr. Walden to Lex about Clark being an alien.

As Clark has finally begun dating Lana, Helen Bryce cancels her wedding to Lex after being told to by Lionel. But later, Helen realizes that she loves Lex and they finally get married. Meanwhile, Jonathan and Martha are thrilled to learn Martha is pregnant. The memory/spirit of Jor-El speaks to Clark via the spaceship, telling him he must leave Smallville, his parents and friends to fulfill his destiny. Clark decides to destroy the spacecraft, and the spirit of Jor-El with it, by using Lionel's kryptonite-made hexagon key that he made a copy of off the late Dr. Walden, in order to use it on the cave wall to learn the kryptonian markings. Clark, with Pete's help, steals the key and uses it to activate the spaceship, knowing the kryptonian radiation will destroy the ship. The ship does explode, but the shock wave injures Jonathan and Martha, causing her to miscarry. Chloe, jealous of Clark and Lana's blossoming romance, accepts Lionel's proposal to investigate Clark and gets the job at the Daily Planet. Clark, grief-stricken at the injury he caused his mother, puts on the red kryptonite ring and heads out of town on a motorcycle, planning never to return. Elsewhere, Lex, flying off on his honeymoon, wakes up alone on the airplane that is about to crash in the ocean...

Metropolis, three months later. Clark Kent (under the influence of the red kryptonite ring) has becomes a criminal, heisting banks, going to night-clubs, and living under the alias 'Kal'. But he comes into conflict with not only his Kryptonian-marked chest, but a ruthless and greedy gangster, named Morgan Edge, who wants an ever increasing percentage of the stolen loot, and also begins to suspect Clark's alien origins. Meanwhile, Lex Luthor is declared dead, but he is living with the weird Louis Leery Jr. in an isolated desert island. Back in Smallville, Dr. Helen Bryce comes to his funeral and meets Lionel Luthor in the mansion where secrets are disclosed. Lana Lang and Jonathan Kent try to bring Clark back to Smalville. Unsucessful after Lana's pleas to Clark, Jonathan makes contact in the cave with the spirit of Jor-El who imbues Jonathan with Kryptonian super-powers to combat Clark and bring him home... in exchange for a price. Also, Chloe enjoys her new job at the Daily Planet, while tailing Lana during her search for Clark.

Lex returns to Smalville and the Lex mansion, and invites Dr. Helen Bryce for a second honeymoon while trying to find out if it was her or his father who attempted to kill him. Meanwhile, Clark also returns to Smallville and the Kent farm, but Morgan Edge finds him and threatens to kill Jonathan and Martha in to get what Clark stole from Lionel Luthor's safe, which is the stolen vial of Clark Kent's blood. With the financial status of the Kent family in dire straights, the farm is sold in an auction, but there is a surprise in the end. Also, Lana tries to declare her love for Clark, but he rejects her love out of fear that she may discover his secret. Clark also returns to Smallville High and to the Torch newspaper under Chloe who continues to investigate Clark's origins.