As if Lois Lane didn't make enough of a nuisance of herself now living at the Kent farm, she brings in Einstein, a golden retriever, who is the latest victim to be hit by her car, and she meanly calls him 'Clarky', while Clark, kind as ever, hopes to keep him as a pet if the owner isn't found, which his parents hope. Clark soon finds out it's a surviving dog of an experiment to give canines superpowers with daily injections of steroids mixed with meteorite fragments (kryptonite) produced at LuthorCorp, which Lex insists to Clark that the project was abandoned after animal activist protests, thinking they were all put down. Only later Clark finds out, the hard way, the dog and a Rothweiler are abused by evil Josh Greenfield and his kid brother Zack, who run the Smalville animal shelter and abuse dog whistles to control the super-dogs as weapons for robberies. Meanwhile, Jason and his secretive and manipulative mother, Genevieve, are revealed to know more about Lex and his apparently reformed father Lionel, while Lana and Chloe all take a keen interest in the relevance of the Teague and Lang family trees, which have common roots in countess-witch Isobel's French place of origin.

When Jason arrives at Lana's apartment at The Talon, they see that is was broken into and wrecked. They discover that the magical stone they took from the Chinese temple is gone. Lana implores Jason to leave it, and concentrate on their romantic relationship instead. But the two meet at Lionel's office, who strongly denies any knowledge of the theft and accuses his son Lex, who makes another innocence-claimant. Meanwhile, the Kent farm gets an uninvited guest's guest: Lois Lane's younger sister Lucy, a violinist who left her fancy Swiss boarding school. The Lane girls start hanging out at Clark's place and at The Talon, where Clark catches Lucy stealing from the till; she says to be in debt with Swiss loan shark Marcus Becker "to afford the lifestyle" of the spoiled brats in her class. Lex knows Becker as member of a major crime syndicate he has business problems with, and offers to help. Becker isn't content to take Lex' money, he kidnaps the sisters to extort more, Clark decides it's time to use his superpowers.

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.

When Lana (possessed by Isobel) kills Genevieve Teague by stabbing her with one of the Kryptonian Knowledge Crystals after she attempts to steal it, it triggers a cosmic event that not only severs Lana's link to the spirit Isobel but also sends meteorites from deep space toward Earth and Smallville. At the graduation ceremony for Smallville High, the military arrives to evacuate the town after news that another meteor shower is imminent. Fearing he has a link to the meteorites, Clark goes to talk to the spirit of Jor-El, who informs him that his only hope is to unite the knowledge crystals in the cave. With time running out, Clark sets about locating the final two crystals as meteorites reign down upon Smallville. Lana gives Clark the third stone they recovered from China, which was in her possession all this time, while the second stone is on Lionel's person, which activates. Lex offers to protect Lana and have her flown to New York City, but she gets caught in the meteor shower while riding in a helicopter. Lois manages to get out of Smallville in time, but Chloe stays behind to follow Clark who retrieves the final one from Lionel which hits them with a burst of energy driving him comatose. Chloe helps Clark retrieve the final stone from the Luthor mansion safe after he is immobilized by kryptonite, and helps him escape from Lex. Clark manages to unite all three stones, which transports him to the wild tundra of the frigid North Pole...

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

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.

While returning home with Lois, Martha is hit by a flash of light followed by a thunder and contracts a lethal Kryptonian disease. Clark fears that Jor-El thus makes him pay for his resuscitation and asks for help from Professor Milton Fine, who tells Clark that Jor-El was a dictator on Krypton, who destroyed their great leader General Zod and the planet but sent Clark to Earth to dominate the world; the death of Martha would only be prevented by destroying the Fortress of Solitude. Meanwhile, Lionel convinces Chloe to investigate who Milton Fine really is. When Lois, feeling offended because Lex called her a "muffin peddler", meets Chloe, the double visits LuthorCorp., where the truth is revealed: Professor Milton Fine is actually a Kryptonian artificial intelligence unit, created by Jor-El but re-programed and corrupted by the Kryptonian rebel General Zod, who was executed for treason, and had his spirit banished to the hell-dimension of the Phantom Zone. Fine, a Brain-Interactive-Construct (aka: Brainiac), is trying to trick Clark into releasing Zod's spirit from the Phantom Zone by destroying the Fortress of Solitude.

On Christmas Eve, Lex travels to a dangerous neighborhood in Granville, Kansas, dealing dirty means to cut Jonathan Kent of the race to the senate. He is shot twice in cold-blood when a couple of junkies steal his car, and Lex has a near-death vision of having a possible middle class lifestyle with a pregnant Lana as his wife and their son Alexander. In his near death experience, Lex is a simple man beloved by the people of Smallville and best friend of Jonathan and Clark. Meanwhile in the real world, he is submitted to a life-threatening surgery ordered by Lionel to avoid becoming crippled. Also, Chloe asks Clark to deliver many Christmas gifts to poor children, and Clark meets a sad and disappointed Santa Claus contemplating suicide. In the end, Lex concludes that love is cursed, based on the fate of Julian, Lillian and Lana, and power and money are the most important values in his life... which leads to him finally starting down the path of the dark side beginning when he secretly orders the execution of the junkie couple who attempted to kill him.

While running for campaign to the senate, Jonathan hires Lois as his advisor. Meanwhile, his opponent Lex is visited by a group of fans lead by the fanatic Samantha Drake, and the deranged woman threatens the safety of Jonathan by attempting to assassinate him at a political rally by using Lois to carry out the deed. Meanwhile, Lana discusses with Clark their sex life on why he no longer wants to make love to her, and Clark exposes his innermost fears to Chloe that Lana will discover his secret superpowers if he continues his romance with Lana. Elsewhere, Lionel takes and eliminates the dossier Griff has prepared to Lex to discredit Jonathan, and offers his financial support to Martha.

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.

When the foster mother and chief of staff of Martha's, Naomi, is brutally murdered, her adopted daughter, Maddie stays with Martha and Clark. The girl becomes close to Clark and speaks for the first time in years. But when she discloses her power to shatter glass, she becomes the prime suspect for the death of Naomi and her biological mother after Lois voices her suspicions to it. While Clark investigates the origin of Maddie, her powerful father, who also has the same ability, breaks out of prison and abducts her. Meanwhile, Chloe witnesses Lex and Lana too close to each other, and later she accuses Lex of taking advantage of the vulnerable Lana.

After "being prepared" by Fine, Lex is abducted in a field by a strange light. Meanwhile, Clark goes to the Fortress of Solidude where the spirit of Jor-el gives a dagger to Clark and advises him to destroy Lex, who would be the vessel of the spirit of Zod outside the Phantom Zone in which Fine, the Brain-Interactive-Construct, is trying to release. Martha travels with Lois to Washington in an airplane of the Luthorcorp. When Zod is released, he possesses Lex, and traps Clark in the Phantom Zone. Fine unleashes a powerful computer virus, creating chaos on Earth. Lois and Martha faint in the airplane without oxygen as another copy of Fine/Brainiac hijacks the plane. Chloe and Lionel are attacked by a raged crowd, while Lex/Zod and Lana declare their love for one another as both plan to travel their path together on the dark side...

Clark enters a parallel environment in his subconscious where he is powerless, no one believes the truth about him, and things have turned out much, much differently.

When Brainiac ends up in a confrontation with Clark after trying to coerce Kara into joining him, he takes it out on Lana.

After being hit by a truck, John Corben becomes a human guinea pig when his heart is replaced by a machine powered by meteor rocks, which, in turn, gives him extraordinary strength, and he realizes he can use it to catch his prey...the Red & Blue Blur.

It is Valentine's Day and while Clark is out on a date with Lois, he unknowingly becomes infected by gemstone kryptonite, which has magical wish-fulfilling properties. Clark mentions to Lois that he wishes they had a more traditional relationship, so Lois quits the Daily Planet, moves in with Clark and starts planning their wedding. Still unaware of his new power, Clark also casually tells Chloe he wishes she would spend more time watching out for him, so an infected Chloe takes his wish to heart and sets her sights on a new target: Lois. Meanwhile, Zod quarrels with Tess as well as his wife, Faora, over the construction of the new solar tower which he hopes will restore his and the Kandorians super powers which will enable them to take over the Earth.

Clark accompanies Tess, who got childhood nightmares triggered by a mysteriously delivered music-box, to the orphanage where she was left behind by her parents. They find out the hard way 'Granny', who runs it, far from her philanthropic image, in fact ruthlessly rules a brain-washed power girls ring. The general finally sent Lois the video made by her late mother when dying from cancer. Dealing with painful and sweet memories, she ends up digging in Clark's Kryptonian parental antecedents in the fortress.

The story of Clark Kent culminates in this two-hour series finale as Clark takes the last step to becoming the Man of Steel.