Clark saves Lana from the tornado, leading Lana to be suspicious of Clark. While protecting Clark's secret, Jonathan gets trapped with reporter Roger Nixon in an underground mausoleum. Lex and Clark search for Jonathan.

When the "hot" new Biology teacher Desiree Atkins (Krista Allen) arrives in Smallville, Clark Kent gets excited in her presence and his hormonal surge sets off a new ability: heat vision. Lex Luthor meets and falls for Atkins and they decide to get married. Meanwhile, Clark's heat vision causes another fire at The Talon when Clark is talking with Lana, leading Clark to get briefly jailed on suspicions of arson. Lex invites Clark to be his best man, but when Desiree tries to seduce Clark, he realizes that she is a meteor freak with the power to seduce men.

When Dr. Steven Hamilton, physically sick from repeated exposure to meteor rock radiation, causing constant Parkinson-like twitches, becomes a liability to Lex Luthor, he terminates their contract. Dr. Hamilton leaves the mansion and drives down the road like a lunatic and causes a serious accident with a truck driven by Ray Wallace. The truck overturns in a cornfield near Clark Kent's spacecraft and, while trying to rescue Ray, Pete Ross sees the UFO. The next morning, Pete asks Clark to help him to bring the object to his workshop. When Dr. Hamilton steals the spacecraft, Pete believes Clark has taken it, so Clark discloses his secret to his friend. Meanwhile, the now blind Lionel Luthor moves into Lex's mansion forcing Lex to care for him. Also, to Lana's dismay, her aunt Nell Potter is in love with a new boyfriend named Dean.

Clark gets his Smallville class ring, but these rings contain RED KRYPTONITE making him turn into DARK CLARK.

Lana Lang finds some poems from a secret admirer in the gravestone of her parents in the cemetery. Later, she meets the author, Byron Moore, a weird teenager kept locked by his parents in the basement of their farmhouse. They believe the boy is abused by his parents, but soon they realize that he was the subject of an experiment of a laboratory of Luthor Corp, which made him powerfully evil and super-strong when he comes into contact with sunlight. Meanwhile, Martha Kent is invited to work as the assistant of Lionel Luthor, and she accepts the invitation under the reluctance of Jonathan Kent.

At Smallville High School, a swimmer mysteriously ages and dies after meeting his girlfriend Chrissy Parker. The new principal Reynolds arrives and comes into conflict with Clark Kent because he is a friend of Lex Luthor's. Clark asks Chloe and Pete to investigate Principal Reynolds' history, as well as Chrissy whom they suspect is a life-draining freak who needs three youths to stay eternally young every 12 years. Meanwhile, the Kents are having financial problems and Martha contacts her estranged father, whom she hasn't seen for twenty years, to borrow some money, much to Jonathan's disapproval. Lana Lang also finds an old picture of her mother with an apparent boyfriend. After not getting any help from Aunt Nelle, Lana then asks Lex to help her investigate.

A woman appears in Smallville claiming that Clark is her biological son by Lionel Luthor, and she kidnaps Lex to force a confession from Lionel. Clark demands that his parents explain what role Lionel Luthor played in his adoption.

Clark rescues mind-reading Ryan James from a research hospital that treats him like a lab rat. Ryan's guardian doctor sues to get Ryan back, and Clark learns that Ryan has a brain tumor that needs treatment.

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.

While practicing motocross with Pete, Clark Kent falls down through a hole in an underground cave and meets a young Native American woman named Kyla Willowbrook (Tamara Fieldman). Kyla is investigating some mysterious ancient paintings in the walls of the cave, and she and Clark immediately fall in love with each other. Her grandfather Professor Willowbrook and some ecologists are fighting against the construction of a Luther Corp building that will destroy the caves, but generate 1,000 new jobs in Smallville. Martha becomes split between the both interests, but the blind Lionel is motivated only by greed and self-interest to keep the project open, while Lana rallies the rest of the town in a protest to stop the construction project. Meanwhile, a mysterious wolf-creature kills a construction foreman, and threatens Martha and the blind Lionel. Following investigation by Chloe, Clark believes that the Professor Willowbrook is a mutant with the power of transforming himself in a wolf. But the real culprit is Kyla.

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.

When Lex Luthor loses a $150 million contract to Luthor Corp, he finds that his mansion was bugged by his father. He hires a team to bug the offices of Luthor Corp expecting to find the building empty since it is Sunday, but Lionel Luthor assigns Martha for work in his office with him. Jonathan becomes very upset, since it is their wedding anniversary, and he was planning a picnic with Martha. Lex calls off the action, but the leader of the group of industrial spies is killed by a member who wants to steal the contents of Lionel's safe. Martha and Lionel become hostages of the criminals, and when they open the safe, a great secret is disclosed. Meanwhile, Lana schedules a meeting with Mr. & Mrs. Small in The Talon to get to know Jennifer Small, who warns Lana about her husband.

Lionel Luthor is shot twice in the Luthor's mansion by an unknown assailant. When Jonathan Kent is found drunk, with a pistol in one hand and a bottle of tequila in the other hand sleeping in his truck, he becomes the prime suspect of the attempt. All the evidences point to him, but Clark believes in his innocence and tries to prove that his father did not shoot Lionel. Clark and Pete team up to investigate leads Lionel had, and learns that the conspiracy to frame Jonathan goes back to the town sheriff. Meanwhile, Lex deals with his father's associate, Dominic Senatori, who thinks Lex was the culprit who shot Lionel, but Lex thinks Dominic is the guilty one. Meanwhile, Lana asks Chloe to investigate Henry Small after he refuses to take Jonathan's case.

During a rave party in the underground cave discovered by the Indian descendant Kyla Willowbrook, the student Travis has a reckless attitude climbing a lamp tower and dies. Soon after, Pete is pierced by a parasite hiding the cave wall, thus becoming reckless and bold. Meanwhile, Lex Luthor hires the linguistic specialist Dr. Fredrick Walden to decipher the meaning of the paintings in the cave. Clark invites Lana to date on the next evening. Later, Clark goes with Chloe Sullivan to the cave, and she is also pierced, changing immediately her behavior. When Pete puts a piece of red kryptonite in the pocket of Clark, he once against becomes 'Dark Clark' or 'Red Clark' in which the trio makes lots of trouble in Smallville and hurts the feelings of Lana.

Lex Luthor rescues his gambler, estranged, half-brother Lucas from a dangerous situation involving Chinese triad gangsters, and brings him to Smallville to help him in a commercial dispute against their father, Lionel. However, Lucas stays side by side with Lionel in his plans of getting his hands on all of Lex's money to feed his gambling habit. The homeless Lex is lodged by Jonathan and his family, while Clark Kent tries to fix the situation with the crafty Lucas before he can carry out his plan to rip off the Luther fortune. But who is playing who? Meanwhile, Clark asks Chloe to put a good word for him to get a job at The Talon which is then bought by Lucas, and Lional reveals that he has regained his eyesight but does not inform anyone.

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.

Clark has some weird dreams with the cave and about flying. When he puts the octagonal key in a hole in the wall of the cave, he immediately learns how to decode the symbols. Then, while waiting for Chloe at the Kents' farm, his uncontrolled vision burns a symbol on the wall of the barn. Chloe publishes the picture in the front page of The Torch, and Clark soon receives an e-mail from a wealthy and prominent scientist from New York. Clark goes to New York and meets the reclusive and quadriplegic Dr. Virgil Swann, who tells Clark about his origins from the planet Krypton, his real birth name of Kal-El. Clark also finds another message in the spaceship which troubles Clark. Elsewhere, Dr. Waldon finds the octagonal key left behind in the cave and when he puts it in the cave hole, he gets hit with the so-called Kryptonian knowledge which overloads his brain and ends up in coma, which further fuels Lex's suspicions about the cave and Clark. Also, Lana considers moving out of Chloe's house to look for a place of her own.

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.

When a van of Luthor Corp is hijacked by three criminals, Clark accidentally witnesses the robbery. He recognizes the leader of the gang, Eric Marsh, a baseball player of Smallville high school. Unwilling to report his suspicious to the pompous Sheriff Adams, who continues intimidating and harassing the Kents, Clark launches his own investigation and discovers that Marsh and his two friends are using refined kryptonite to use as inhalers to give them super-human strength. Meanwhile, Clark quits his job at school paper, The Torch, after discussing with Chloe about him missing a few too many deadlines. Lana sees Jennifer Small with her lawyer, and she tells Lana that she plans to divorce Henry Small. Also, Lex tries to find what cargo was stolen from his father by trying to follow Eric Marsh, while Lionel arrives in Smallville for a surprise visit to Lex, and to Chloe whom he offers her a job as an intern at the Daily Planet newspaper in Metropolis.

Lana sees the impossible: a friend named Emily Eve Dinsmore, who died six years earlier in a fatal accident at age 10, and still appears that age. Clark Kent believes Lana and searches for the truth. Emily's father Mr. Dinsmore has an accident provoked by Emily and Lionel Luthor visits him in the hospital. Lana and Clark eventually discover that Emily is the result of a Luthor Corp experiment in accelerated cloning. But problems in her chromosomes have caused her to be a flawed copy, resulting in a bad temper, with the power of super-speed and telekinesis. Meanwhile, Lex Luthor plans his wedding with Helen, while Lionel gives Lex a free airline ticket for a honeymoon in the Caribean, and to tie up some loose ends over the Emily cloning matter, and to take control of the old cave away from Lex.

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...