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.

When Lana is attacked by her obsessed school pal Jake Pollan in the deserted swimming pool of Smallville High School, he is mortally shot by an unknown shooter. Meanwhile, Lex Luthor joins Luthor Corp. and his father, Lionel, requires a $50 million life insurance from him which increases Lex's suspicions. Clark investigates the murder of Jake, and finds that the criminal is Jake's friend Van McNulty, who is killing people affected by the meteor rock radiation, and Lex is the next in his death list. When Clark saves Lex, Van sees that he is special and includes Clark in his bill, and learning of his vulnerability, the growingly paranoid and racist Van concocts and shoots Clark with a kryptonite bullet, and then decides to go after Lana for her association with Clark. Also, Chloe discovers that Lionel has taken all her research documents of Clark after discovering that she has begun investigating Lex.

Clark's future boss at the Daily Planet shows up; Perry White, but this time around he's a dirt bag reporter working for the tabloids.

Clark has downloaded the memories of Jor-El to solve a case that is related to Lana Lang's relative.

After being hit in the forehead by a snow globe containing flakes of meteor rocks in a struggle at a local carnival, the teenager Seth Nelson is given an M.R.I. giving him magnetic abilities. He uses his powers to date and manipulate Lana who is starting to distance herself from Clark by trying to make him jealous. Meanwhile, a snoopy investigator hired by Lex intrusively breaks in The Torch and finds that Chloe Sullivan is examining deeply the life of Lionel Luthor. Lex offers his protection to Chloe to help him investigate his father's past if he had anything to do with a apartment tenement fire that killed Lionel's parents.

While looking for a birthday gift for Martha at a local jewelry store, Clark intervenes when two thieves try to rob the place using the powerful scream of Nathan Dean (Micah Alberti), a meteor-rock mutant with the ability to project ear-splitting screams. The combination of the scream with a bijouterie of kryptonite deflecting Clark's heat vision back to his face makes Clark blind. Without this sense, his hearing uncontrollably increases. One of the criminals, Masterson (William MacDonald) is arrested. Nathan kidnaps Pete to force his mother, Judge Abigail Ross (Felecia M. Bell), to release Masterson. Meanwhile, the blind Clark listens to a phone conversation between Chloe and Lionel Luthor about Lex and himself. After Clark informs Lex about his father's intentions for them, Chloe is mistakenly taken as Lex's informer and she gets fired from her intern job at the Daily Planet by Lionel.

After leaving an article full of denunciations about the "Summerholt Neurological Institute" with her former colleague of the Daily Planet, Max Taylor, Chloe is chased by Clark Kent who tries to run her down with his truck. He claims that he had received an e-mail just before his action. Later, Lana also receives an e-mail from the same address and tries to kill Chloe on the steps of Smallville High, who is saved by Adam Knight. Clark and Chloe, with a little help from Lex, investigate the mysterious e-mail origin, and they discover that Molly Griggs, a former patient of the unethical Dr. Garner, is using her meteor-rock abilities to force people to kill through a hypnotic suggestion in her e-mails. Meanwhile, Adam moves to Smallville to be close to Lana despite that nobody knows anything about him. Also, Lex makes contact with Dr. Garner and threatens to expose his unethical practices unless he helps him regain his memory of the last seven weeks.

Jordan Cross is a new transfer student to Smallville High School who has a frightening ability: when he is touched by another person, he immediately sees how he or she will die. When Clark saves the suicidal Coach Altman from death, the future of other people changes, including Lana's. Jordan also learns Clark's secret after he physically bumps into him. Meanwhile, Chloe finds that Adam is injecting himself with some kind of experimental medication, while his increasingly erratic behavior troubles Lana. When Jordan touches Adam, he tells Lana that Adam had already died. Also, Lex continues to investigate his past to regain his memory.

While returning home after leaving Jonathan Kent in the hospital recovering from a heart attack, the truck of Martha and Clark is almost hit by two cars racing in the road. For the greatest surprise and deception of Clark, one of the drivers is Pete Ross, who has become the friend of the bad element Jason Dante whom is using meteor-rock synthetic fuel to win at drag races. Pete does not accept Clark's advice and gets into serious trouble when Dante wants $20,000 of losses after thinking Pete betrayed him to the police. Meanwhile, Lex investigates the prominent Dr. Lia Teng about her research of blood platelet with Adam Knight, and Lana feels threatened by the mysterious dark secret of Adam after finding out that he "died" of a rare liver disease and learns about the mysterious blood platelet drug he is taking to keep himself alive.

While in an elevator at Luthor Corp with another girl during a class field trip, Clark is forced to use a few of his abilities when the cable of the elevator accidentally breaks and in the process, the student, Alicia Baker, witnesses Clark's ability of heat vision and punching through steel and in return, Alicia 'teleports' herself and Clark out of the elevator. Clark confides his secret to Alicia who confides her secret of being a meteor-rock mutant with the ability of teleportation. Soon, Clark and Alicia start to get closer and he starts to really think that Alicia could be the one for him. But Alicia on the other hand, turns out to be an obsessed sociopath who wants Clark... NO MATTER WHAT! When Clark starts to realize Alicia's obsession with him, he decides to put an end to their brief relationship. But Alicia won't settle for second and sets off to kill Clark's true love Lana. Elsewhere, Lana finds a journal that Adam has and finds out that he has been spying on her and Clark... under orders from Lionel. So, Lana turns to Lex for help with this situation.

When Jonathan goes to Smallville Medical Centre for a physical examination, his doctor diagnoses arterial blockage and recommends a triple bypass heart surgery procedure. Meanwhile, Vince Davis, the older brother of Clark Kent's friend Garrett Davis, needs a liver transplant - but does not receive one and he dies. His body is sent to Metropolis to be the next test subject of Lionel's experiment by Dr. Lia Teng, who injects his dead body with experimental blood platelets and revives him. When Vince gets sick again (because he needs the life-sustaining blood injections on a daily basis), the unstable Garrett loses control and becomes a threat to the patients, employees, and visitors of the hospital by showing up at the hospital with a kryptonite-infused bomb strapped to himself, threatening to blow himself up unless his brother receives a new liver transplant. Clark must try to find a way to defuse the situation during Jonathan's heart surgery, while the overzealous Sheriff Adams wants to kill Garrett in any way possible... even at the expense of the hostages. Meanwhile, Chloe does some investigating for Lex of Dr. Teng and learns about the mysterious blood platelet serum she's manufacturing and about the first test subject: Adam.

While working as a volunteer with Pete at Smallville Youth Center, Clark receives a distress phone call from Lana, who is shot by Adam. His further investigation shows that the call was made from the future because of a time/space porthole created by a massive electrical surge from a downed power line fitted with meteor rocks, during a coming thunderstorm. Clark must try to save Lana and change the future. Meanwhile, Lionel Luthor shuts down the obscure Merton Laboratory and the research that Dr. Lia Teng is developing with blood platelet, which were finally revealed to have been developed from the vial of Clark Kent's blood. Adam becomes aware that he has less than 12 hours to be injected with the serum, otherwise he will die. He escapes, kills Dr. Teng and her whole team, and Lex is framed as responsible for the mass murder. Adam then sets out to find Lana to know if she still has an extra vial of serum for him. Lex later meets with an FBI agent, named Frank Loder, who enlists his help to bring down Lionel Luther, who also confides in an associate of his about his research and reveals the reason for it: Lionel himself is dying from a rare liver disease.

When Lana is attacked in her apartment and Jason in his car by an invisible being, everyone believes that Alicia Baker was responsible, except Clark. However after a series of circumstances, Clark begins to doubt Alicia's innocence to the mysterious attacks. Alicia tells Clark that she'll offer to prove her innocence if Clark reveals his own superpowers, but Clark refuses. So, Alicia secretly shows Chloe the abilities of Clark, expecting people to leave them both alone. But elsewhere, Lois discovers that the real culprit of the attacks is the deranged Tim Westcott who's jealous of Alicia's abilities which leads to him murdering her, and then goes after Clark. Meanwhile, Genevieve Teague arrives back in Smallville and approaches Lex Luthor to get his help to separate her son Jason from Lana.

It's almost graduation, and that means it's time for the prom. After a car accident, a meteor-infected student in-the-run for Prom Queen starts body-swapping. Meanwhile, a dead body is found on Lex's mansion grounds.

Kevin Grady commits thefts and uses his superpower to delete the incident from witnesses' minds. When he does so with Clark who stopped him after robbing The Talon, much more memory gets wiped, so Chloe must take super-boy home to the Kent farm and help him remember who he is, including discovering together the amazing extent of his superpowers and his feelings for Lana Lang. Meanwhile Lana tells Jason she's neither sure she still wants to go to college nor to stay his girlfriend, claiming it's not Clark but their complicated past, he walks off angry, warning she doesn't realize how much he has been protecting her. Clark and Chloe trace a motor-park pass Kevin dropped to his home, or rather to his father Lawrence Grady, and gradually discover Kevin is in memory manipulation therapy with him in Summerholt neurological institute, where Lex once was a patient, for a hunting accident killing his brother Dillon but escaped. Clark helps Kevin...

In the middle of the night on the road, a young pregnant woman is going into labor while the father of her child drives, when she suddenly glows and implodes, while the guy stops the car and runs for his life. Lana and Clark are driving a truck along the same road and find a baby in the crater created by the explosion. They take the baby to the hospital, and the Kent family temporarily guards him, who is connected to Clark. Lana and Clark give the name of Evan, and on the next day, he becomes a teenager, precociously aging. The scientists of Lex study the case and conclude that the boy needs a transfusion of the bone marrow of his unknown father, if he can be found, and even then... Clark tries to save Evan. Meanwhile, Genevieve Teague has a meeting with Lionel Luthor and threatens to hurt Lex, in case the missing stone from China is not delivered to her. But Lionel soon turns the tables on Genevieve by poisoning her (the same way he unsuccessfully tried to poison Lex in the previous season) and threatens not to give her the antidote unless she gives him the second missing stone whom she in fact stole from the murdered Bridget Crosby.

A meteor shower bursts from the heavens, raining destruction on the unsuspecting citizens of Smallville, Kansas.

After Clark lost his powers, he finds that he needs them the most to save his family.

Gabriel Duncan is a deranged teenager who breaks in the control room of a nuclear silo in Smallville, kills the two security guards, and starts the launch sequence to send one missile to destroy Smallville in one hour. He calls his friend Chloe, who is moving to the university, and asks her to leave the town that he wants to destroy because of the population of "meteor freaks." The army does not know which of the sixteen silos might have been broken in by Gabriel. Meanwhile, Clark and Lana sleep together in his room and early in the morning, Lana sneaks out of the house, but Jonathan and Martha see them. When Chloe calls Clark, he plots a simulation of a car accident with Chloe to force Gabriel to disclose his position. When Gabriel meets Chloe, Clark is deadly shot by the insane teenager, dying in the hospital. Suddenly, Lionel Luthor awakes from his catatonic situation in Belle Reve and Clark's body vanishes from the hospital which leads to both meeting at the Kryptonian Fortress of Solitude at the North Pole which leads to a surprising discovery for Clark. Elsewhere, the evil Lex continues to obsessively study the black spaceship at the LutherCorp warehouse and discovers that something else has climbed out of the ship.

A deranged policeman who survived the attack of the Kryptonians and his policewoman fiancée break into Lex's mansion asking for the location of the spaceship so they can go public with the news of "aliens on Earth". But Lex locks himself in the panic room. Clark accidentally finds the association of Lana with Lex in their research of the spacecraft when Lana is kidnapped by the renegade cops to force Luthor to leave the room. Lex gets shot, but Lana escapes to the panic room with him. Meanwhile, Jonathan presses Lois to find out who is funding his campaign and Martha tells the truth about Lionel.

Clark is shown by Jor-El what life on Earth would have been like, had he not sent him there instead of facing the doom of his fellow Kryptonians.