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.

Clark meets Arthur "AC" Curry, a young man with extraordinary powers underwater. AC is in Smallville hoping to sabotage a Luthorcorp experiment that is threatening sea life. While in Smallville, AC forms an attraction to Lois.

Lana tells Clark that she is moving to the Metropolis University and she is accepted in the Tri Psi Sorority, a sisterhood with hot vampires led by Buffy Sanders, and Lana is transformed in a vampire. Meanwhile, the chief-editor of The Daily Planet, Pauline Kahn, denies an intern position to Chloe, but in the end she proposes Chloe to write a good story to prove that she might be part of the team of reporters. Meanwhile, Lex intimidates Professor Milton Fine, but in retribution he shows a dossier about the secret experiments that Luthorcorp is performing in the campus of the Kansas University. When Clark sees Lana at Chloe's room, he believes she is with a hangover; later, he goes with Lana to a Halloween costume party promoted by the Tri Psi. When Lana attacks Chloe, Clark discloses the truth about Buffy and her sisterhood of vampires and tries to find a means to save Lana and Chloe when she gets bitten by the evil vamp Lana.

While working in the night shift at the Daily Planet, Chloe receives a distressed phone call from a woman claiming that she is in danger. Chloe and Lois schedule a meeting with the woman, but a car runs over her and the cousins witness the murder. Meanwhile, the close friend of Jonathan, Senator Jack Jennings, visits the farm to rest from his campaign for the senate against Lex Luthor. Jonathan is surprised by the visit of Detective Maggie Sawyer, who is investigating the death of the nineteen-year-old stripper that Chloe and Lois witnessed last night. She found a picture of Senator Jennings with the girl and is following the lead. Clark believes Lex is involved with the crime, but Lex helps him in the investigation. Lois decides to go undercover by working at the nightclub as a stripper to investigate the murder. When Lois meets the criminal, she is abducted and her life is in danger.

While visiting Lana in Metropolis, Clark opens a package addressed to Lana apparently sent by Lex Luthor and is wounded and infected by a splinter of silver kryptonite. This unusual piece of kryptonite causes Clark to have paranoid delusions, and he sees Chloe, Jonathan, Martha, Lana and Lex plotting against him. He defends himself against his "enemies", jeopardizing the lives of his dearest friends and family. But eventually help comes from a most unlikely of source: Milton Fine.

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.

Clark reveals his secret to Lana, Jonathan and Lex learn the results of the senatorial election, and there is a tragic car accident on the highway that takes the life of someone Clark loves, forcing Clark to appeal to Jor-El for help.

Clark Kent drops out the rest of the semester from Metropolis University to help Martha on the farm. He misses Jonathan and has not superseded the loss of his foster father. Martha offers Jonathan's watch to Clark, but he refuses. Martha goes to Metropolis to donate Jonathan's belongings to a mission, and she is assaulted by two lowlife criminals. However, she is rescued by a masked and powerful vigilante, but one of the punks steals the watch. Clark feels guilty about the watch and visits Chloe, trying to track the muggers. They decide to find the 'Angel of Vengeance,' and when they meet her, she discloses her identity of Chloe's klutzy colleague Andrea Rojas and tells that she became powerful six months ago after a heart transplantation of a donate that was hit by the meteor shower. Her mother and she were attacked by a mugger who killed her mother while Andrea survived, thirsty of revenge against the killer of her mother. Clark joins Andrea, but with a different viewpoint of justice since Andrea believes in killing criminals who have gotten away with murder through legal technicalities, whereas Clark still believes in the court system despite it not working most of the time. Meanwhile, Lionel tries to take the LuthorCorp from Lex, but he is blackmailed and gives up his intention.

During a power blackout, Chloe sees the ghost of a girl and cuts her both wrists. Chloe is interned in the hospital, and the psychiatrist diagnoses that she had a breakdown due to stress. Lana asks Lex to send Chloe to a mental institution for treatment since nobody believes her. However, Clark brings his friend to Lois's apartment above The Talon, where Chloe is possessed by a spirit of the dead girl, called Gretchen, and shows Clark the place where the skeleton is hidden in the Talon's wall. Chloe leaves the apartment alone seeking revenge against the killer, while the deranged orderly Michael Westmore kidnaps Lois. Meanwhile, Clark researches for information about the death of Gretchen in old newspapers. Also, Lionel encourages Martha to take the late Jonathan's place as senator to move on with her life.

After being released from a prison in a laboratory of Luthorcorp's Cyntechnics by sympathetic scientist Dr. Hong, former Metropolis High football player Victor Stone is chased by armed security guards and hit by Lana's truck, without any harm. The car is totally destroyed, Lana wounds her forehead and Victor takes her to a hospital. Lana calls Clark, and he meets Victor, who played football against him in high school and died a year ago in a car crash. Victor explained that he became a living machine as part of the machine project researched by the evil Dr. Allister Krieg sponsored by Luthorcorp. Further, he misses his girlfriend Katherine. Clark promises to help him and visits Lex, who lies and tells Clark that he was not aware of the project. Meanwhile, Martha is blackmailed with a DVD showing Clark on a security camera rescuing the unconscious Lana from the warehouse explosion (from episode 'Lockdown') and Lionel offers to help her find the blackmailer.

Simone, a gorgeous blonde, comes to Smallville hypnotizing Clark with a blue pendant ruining his relationship with Lana, as well as hypnotizing Martha and Lex.

The lonely Lana gets addicted in a meteor rock cocktail developed by her new acquaintance student of medicine, Lance, which allows the user to have a near-death experience and visit the dead loved relatives and friends. Meanwhile, Clark goes to Honduras, where there is a massive destruction, trying to find Milton Fine and the spacecraft after following a lead from Chloe. When Lana gets in trouble, Clark returns to Smallville but is injected with the serum. In his trip, he meets Jonathan, who tells him that Lionel Luthor knows his secret, while Martha gets close to 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.

Lionel Luthor is chased by a man with a mask and forced to play hangman to save his life when he traps Lionel in his limo in the path of a moving train. Later, he is abducted by the same stranger who places Lionel in an abandoned warehouse where he has to play lethal 'Jigsaw' type games to survive. Martha is also kidnapped and in his last test, the life of Martha is also put at stake and Lionel has to fight to save her life. Meanwhile, Chloe, Clark and Lex join forces trying to find Martha and Lionel.

Standing outside the Metropolis courthouse with Chloe, Clark saves Graham Garrett from a car which would have crushed him. Graham insists to repay the favor by offering Clark whatever he wants, including the opportunity to be with Lana again. Graham later turns out to be a hired killer with chameleon powers that render him invisible. Clark also gets angry at Chloe for keeping Lana and Lex's affair from him. When Clark realizes that Graham wants to kill Lex and Lana to protect his identity, Clark rushes to find and ptotect them both.

Jonathan Kent appears to Clark on his birthday and instructs him that he needs to kill Lionel Luthor because Lionel knows his secret. Meanwhile, Lionel comes clean to Martha about his knowledge of Clark's secret since his possession by Jor-El, and some of his scribblings from his now-telepathic link to Jor-El are revealed to announce that the "Vessel of Zod" is coming. Meanwhile, Lex has another meeting with Milton Fine who tells Lex that he is trying to make a vaccine to protect mankind against an alien virus. When Lana expresses suspicion that Fine is not who he appears to be, Fine reveals his real identity and that "Jonathan Kent" is just another copy of Fine (The Brainiac) sowing seeds of anxiety in Clark.

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...