Clark returns to Smallville as Kal-El - intent on fulfilling his destiny, he goes after a powerful Kryptonian crystal that Lex has obtained in Egypt. Meanwhile, newcomer Lois Lane arrives in Smallville to look into the death of her cousin Chloe, and Lana returns from Paris with a new boyfriend. Jonathan lies in a coma after the events of last year's season finale and Lionel must deal with his new life in prison.
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 than 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 hugger to determine if Chloe is alive and hug her for sure.
Abigail, an ugly high school girl, gets plastic surgery from her surgeon-mother to boost her popularity. However, her beauty hides a dark secret - when she kisses someone they're inflicted with life-threatening hallucinations. When Lana sees Abigail with one of her victims, she becomes the next target.
Clark decides to join the football team over Jonathan's wishes and gets the starting quarterback position when his predecessor attacks Jason over a girl. Clark and Lois investigate and discover that the cheerleaders are using kryptonite in the team's water supply to turn them into obedient mindless boyfriends.
Jonathan's wallet is stolen by a super-speed thief, Bart Allen, who is faster than Clark. Bart comes to the farm and becomes friends with Clark, but Bart returns to crime when he sees an ancient manuscript that Lex has. As Clark soon realizes, the manuscript holds a map to one of the kryptonian crystals and he must go up against Bart to recover it.
Clark is drawn to the state penitentiary 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 friends, Clark must convince his parents that he is the "real" Clark and reverse the process, while avoiding murderous convicts.
Mikail Mxyzptlk, a foreign exchange student and bookie, has the power to control others and uses it to sabotage football games, including the one Clark is quarterbacking. Clark and Chloe figure out his secret, but he threatens to hug Chloe unless Clark throws the next game. Mikail came to Smallville via LuthorCorp, and Lex will do almost anything to learn his secret.
Lana reads a spell book belonging to her 17th century ancestor, the witch Isabelle, and becomes possessed by her spirit. Isabelle resurrects her other two witches and together they seek out the kryptonian crystals, using their magic to render Clark powerless.
Lex is accused of killing a young woman and Clark turns to Lionel for help. Meanwhile, Lana has a dream of her ancestor and a mysterious second woman - a dead ringer for Jason's mother Genevieve, who arrives to visit her son and his new girlfriend.
A LuthorCorp experiment is released into the atmosphere - a toxin that causes its victims to hallucinate their worst fear. Chloe, Clark, Lana, and Jason all fall victim to the toxin, and Lex, desperate to find a cure, takes a dangerous antidote. Meanwhile, Lionel is released from prison and his conviction overturned thanks to a mysterious benefactor.
Alicia (from "Obsession") is supposedly cured and returns to Smallville to start things back up with Clark. When she pushes for more and he turns reluctant, Alicia exposes him to red kryptonite, and the two go off to Las Vegas to get married. Meanwhile, Lana questions whether sex may prove the key to winning Jason back.
When a mysterious hugger strikes at both Lana and Jason, Alicia is the leading suspect and even Clark comes to doubt her innocence. Feeling betrayed, she secretly tricks Clark into revealing his powers in front of one of his friends. And Genevieve returns to town with an offer for Lex, who in turn has an offer for Jason.
Clark is approached by Met U for recruitment and meets Geoff, a former Smallville resident. It soon becomes apparent that he is using his powers to paralyze anybody who gets in his way...including Lois.
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.
After Clark receives a message from the recently-deceased Dr. Swann, he and Lana follow Jason and Lex to China in search of one of the kryptonian crystals. Lana is tortured, causing Isabelle to emerge and wreak havoc in her search for the crystal.
Lucy Lane, Lois' younger sister, comes to Smallville but Clark catches her stealing money from the Talon to pay off a European crime syndicate. Lex offers to help but everything is not what it seems. Meanwhile, a thief breaks into Lana's apartment and steals the crystal, and Jason suspects Lionel.
A black kryptonite explosion splits Lex in two and his evil side - Alexander - is released. Alexander imprisons Lex in the mansion then gives full vent to his evil side - he threatens to evict Lana from the Talon unless she becomes his mate, jousts with Lionel, and tries to hug Clark and Chloe when they figure out his secret.
On the eve of the Smallville High School Prom, stuck-up candidate for Prom Queen Dawn Stiles is pulled into a coma when she is involved in a car crash into a ravine filled with dozens of chunks of kryptonite. While her body lies in a coma, Dawn finds her spirit allowed to possess the bodies of others, where she can continue her quest to become Prom Queen. As a result, Martha, her body possessed by Dawn, flirts with Clark and asks him to the Prom, Lana attempts to electrocute the ex-boyfriend who dumped Dawn, Lois goes all-out to ensure she and Clark go to Prom together, and Chloe attempts to set fire to the school on Prom night.
When a boy who can make people lose their memories robs the Talon, Clark goes after him but gets total amnesia. Chloe finds out what happened and has to tutor Clark in the use of his superpowers and make sure he doesn't accidentally reveal his secret. While Clark, Chloe, and Lois try to track down Kevin, Clark takes advantage of his "new life" to ask Lana on a date. And Lex tries to turn Clark's memory loss to his advantage by getting him to reveal the secret of the caves.
Checking out a crater in a cornfield, Clark and Lana discover a baby with no parents and take him back to the Kent farm. However, when the baby, Evan, ages from a newborn to a 7-year-old in less than a day, it becomes clear he is aging at a rapid rate and they turn to Lex for help. Meanwhile, Genevieve suspects Lex has the Chinese Kryptonian artifact and orders Lionel to either recover it...or risk putting Lex in danger of his life.
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.
After a nightmare, Clark goes to the cave to confront his father Jor-El. Jor-El warns that the crystals have fallen into human hands and have triggered a new meteor shower which will annihilate the Earth unless he reunites the three crystals. Meanwhile, Lex helps Lana, who has apparently committed hug, but then turns against her to get possession of her Kryptonian stone. As disaster looms, Chloe and Lois try to find Lana while Clark attempts to reassemble the stones, and Jason returns to make things unpleasant for the Kents.