A flower that comes from a reopened "Level Three" of the fertilizer plant brings strange reactions from several people, including Jonathan, Lana, and Pete.

Former Smallville High cartoonist Justin loses the use of his hands in a hit and run accident, and develops the ability to move things with his mind. After crippling his unsympathetic doctor he returns to Smallville and hooks back up with his friend Chloe. He reveals his secret to Chloe, and then takes revenge by killing Principal Kwan, who was the driver who hit him. It turns out Kwan's son Danny was the driver. Chloe realizes Justin is responsible, and Clarks comes to her aid, knocking Justin out. Meanwhile, Lex's former nanny, Pamela, comes back to see how he's doing and to apologize for leaving him after his mother's death, bringing up some old issues for Lex. And Whitney's father passes away.

Clark gains a new power - heat-vision. As he struggles to control it, Lex gets married to the new Smallville High teacher, Desiree Atkins, little does he know that she not only has an alterior motive, but that she's coming on to Clark too.

Lex hires some thugs to bug Lionel's office but things get out of control when Lionel and Martha are taken hostage, and Clark must rescue them without revealing his secrets.

Clark travels to New York to meet Dr. Swann, a brilliant scientist who holds a message for Clark from his home planet. Meanwhile Lana decides to move out of Chloe's house after they get into an argument about Clark.

Lana is haunted by the ghost of a dead friend, Emily, but the "spirit" has connections to Lionel Luthor, who is also scheming to get control of the Indian caves and "help" Lex with his wedding.

Clark gives up the ring and its effects rather then kill his father, and both he and the rescued Lex return to Smallville. Clark must deal with crime lord Morgan Edge, who has followed him to Smallville, while Lex must determine who tried to have him killed - Lionel or Helen.

Clark discovers that his schoolmate Jordan can foresee the future, but is horrified when Jordan tells him he "sees" Lana dying in a fire in the next few days. Meanwhile, suspicious of his behavior, Chloe investigates Adam's background and discovers some disturbing news.

Clark is forced to use his powers in front of Alicia, a new girl at school, but he is surprised to find out she has powers of her own. The two develop a bond through their shared secret, but things turn ugly after Alicia becomes obsessive about sharing Clark with anyone else - especially Lana. Meanwhile, Lana asks Lex to investigate Adam.

When Chloe accidentally inhales a mysterious krypto-gas, she discovers it acts as a truth serum to anyone who comes in contact with her and decides to take advantage of her new power by going to the Kents to find out Clark's secret. However, her new power comes with fatal consequences and Clark must find an antidote before she discovers the truth about him or worse, dies.

After discovering that Chloe's body isn't in her coffin, Clark and Lois Lane investigate but are stopped by Lois' father, General Sam Lane. They believe General Lane knows more then he's telling, and figure out he's been in contact with Lex. Meanwhile, after Lana's sudden departure Jason follows her to Smallville. And Lionel sends a mutant killer to determine if Chloe is alive and kill her for sure.

Clark is drawn to the state penitentery by one of the kryptonian crystals, which Lionel is using to switch bodies with Lex. Clark intervenes and Lionel enters his body instead. While Lionel uses his newfound super-powers to regain his lost fortune and alienate Clark's friend, Clark must convince his parents that he is the "real" Clark and reverse the processs, while avoiding murderous convicts.

Lois accidentally hits a dog and brings it back to the farm to heal, but Clark quickly realizes it has super-strength. He investigates and discovers it was part of an aborted LuthorCorp experiment...and that robbers are using the dogs to help them steal money. Meanwhile, Lana wonders what Jason is up to with his mother, and Jason is forced to ask Genevieve a few questions of his own.

Clark must stop the school photographer after he sets up a fake high school and uses his ability to petrify people to kidnap students - including Chloe and Lana - to keep the glory days of high school going forever. Meanwhile, Lex and Lionel are kidnapped and tortured by the Teagues in an effort to find the Kryptonian artifact, revealing that...Lana has it.

Having been transported to the Fortress of Solitude, Clark is confronted by Jor-El, who tells him he cannot return to Smallville, instead he must stay and prepare to save the planet. Also, transported to the Fortress, Chloe is unable to handle the sub-zero temperature and collapses, begging Clark to use his powers to save her. Jor-El forbids him to leave, but finally acquiesces, telling Clark he must return before sunset or there will be dire consequences. Meanwhile, Lana is horrified when she sees two Kryptonian aliens emerge from a spaceship discovered in the remnants of the meteor shower. The two aliens destroy what's left of the town searching for Kal-El.

Clark gives into paranoid delusions brought on by exposure to new "silver" kryptonite, and Professor Fine is the only one who can save him... before he kills Lana.

Lionel is taken hostage by a masked man who forces him to play elaborate games for the prize of staying alive. Martha goes to confront Lionel after Clark tells her Lionel knows his secret and becomes a part of the game herself, fighting for her life.

Professor Fine has unleashed a virus that will kill millions. Clark must put a stop to him, while Lex wonders what happens when he will tell Lana his newest secret.

A powerless Clark is trapped in the "Phantom Zone" surrounded by the criminals his father imprisoned there. However, an unexpected ally comes to his aid. Meanwhile, Zod in Lex's body advances his plan to transform Earth into a new Krypton, while using Lana to produce an heir.

Clark and Chloe find an escaped Zoner named Titan who is the star of a secret fight club that puts its death battles on the internet. Lois can tell that there is a story and goes to investigate, where she is put in the ring to fight. Clark goes in as a super-powered fighter to take on Titan but ends up against a different opponent instead.

Clark discovers the reason Lana married Lex then and sets out to kill Lionel. Lex tries to use DNA from the last phantom to power his super-soldiers. Lois goes to a dam to search for Lex's lab but is caught by a security guard and fatally injured. Chloe's power is discovered.

Lex tracks the amnesiac Kara to Detroit, where Lois follows him. An obsessive busboy infatuated with Kara shoots Lex, and Chloe has to determine whether to heal him or not.

Clark must learn a new superpower as he and Kara join forces to take on Brainiac, putting the lives of their friends in danger.

Tess tries to kill Davis by blowing up his truck. However, after he escapes, she realizes she needs help to destroy him and turns to Clark. Tess reveals Davis' secret childhood with the Luthors and hints that she knows Clark's true identity. Meanwhile, Davis runs to Chloe for help.

Oliver tells Clark he must kill Davis, as Doomsday is a serious threat and must be stopped at all costs. However, Clark struggles with taking a human life, so the Green Arrow and his team decide to take matters into their own hands. Lois takes on Tess, but the fight takes a shocking turn. Meanwhile, Chloe gets caught in the middle of Oliver and Clark’s battle over killing Davis.

Lois decides to tell Clark she knows he’s The Blur, but she accidentally activates an ancient artifact that transforms her into the Goddess Isis, complete with superpowers of her own. Oliver and Clark reluctantly decide to ask Tess for help with Lois. Meanwhile, after Cat Grant witnesses Lois as Isis using her superpowers, she decides Lois is the Blur and sets out to prove it.