Clark rescues Lana from the storm, but discovers that the spaceship is released, while Jonathan is buried alive with the unscrupulous reporter who discovered Clark's secret. Meanwhile, Lex is wracked with guilt over his critically injured father.
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 ulterior motive; but that she's coming on to Clark, too.
Pete finds Clark's spaceship, forcing Clark to reveal his secret to his best friend. Dr. Hamilton is plagued by kryptonite-fueled illness and focuses on Pete. Meanwhile, Lana has to deal with Nell and her plans to remarry while Lex and Lionel adjust to life together.
Clark has his first run-in with red kryptonite in this exploration of classic Superman mythology, turning immoral when he gets his high-school ring holding a piece of rock. Meanwhile, Lex and his father have some issues to resolve when Lionel starts taking over the manor.
Lana has a new stalker - a boy imprisoned in his basement by his parents who sneaks out at night to visit her. Meanwhile Lionel hires Clark's mother as his personal assistant.
Martha's father William comes to town after many years of estrangement due to his disapproval of Jonathan. Meanwhile Clark must deal with a series of old-age deaths at Smallville High, and the new principal puts his foot down.
A strange woman shows up claiming to be Clark's biological mother...and that his father is Lionel. Meanwhile Lana decides to meet with the man who is her biological father.
Ryan (from "Stray") returns and Clark has to save him from Dr. Garner of the Summerholt Research Facility. Meanwhile, Aunt Nell leaves Smallville, and Lex wants to expand the plant but runs afoul of the mayor.
A Smallville student, Ian, displays the ability to make clones of himself and uses his power to date both Choe and Lana. Meanwhile Lex goes to anger management class and meets an attractive local doctor.
Clark becomes involved with a Native American woman, Kyla, and becomes aware of ancient Indian prophecy that warns of a man of great powers who fell from the sky. Worse, a wolf-like creature is attacking the local Luthorcorp construction project, and Martha and Lionel may be the next victims.
Whitney returns to Smallville, eager to start back up where he left off with Lana. But everything isn't what it seems...
Meanwhile, Lex gets suspicious with his relationship with Dr. Bryce, only to find that she has been having meetings with Lionel.
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.
Lionel is shot in the manor, and Jonathan is the prime suspect.
Students are engaging in wild, sometimes suicidal stunts, and Chloe and Pete are the next ones to become "infected"...and they use a piece of red meteor rock to get Clark to join them.
Lex recovers his long-lost brother Lucas and uses him in a ploy to buy out his father's share of the company. But it soon becomes clear that Lucas isn't to be trusted, and Lex soon finds himself ousted from his own company.
Martha catches a lungful of kryptonite-irradiated spores and slips into a coma. Clark, who temporarily loses his powers by breathing in the same spores, is her only hope for survival. Lex sneaks behind Helen's back at the hospital in his continued search for the truth about Clark.
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.
After a schoolmate claims to be an alien and proves it by using heat vision, Clark investigates and believes the boy is from Krypton. Meanwhile, Helen confronts Lex over the locked room in the mansion that holds his investigation of Clark's secrets.
After Lana is almost assaulted by a college student, Clark injures the boy while helping her. When the Kents are sued for damages that could cost them the farm, Clark tries to find a way out of the lawsuit. Meanwhile, Helen's obsessive ex-boyfriend comes to Smallville to win her back but when she turns him down, he stabs her, prompting Lex to take the law into his own hands.
Clark runs up against super-strong robbers who are apparently tied to LexCorp. And Chloe begins to ally with Lionel, while Lana and Henry Small bond.
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.
Dr. Walden comes out of a coma with super-powers and a desire to hug Clark, piquing the Luthors' interest. The spaceship starts talking to Clark, and Helen and Lex prepare for their wedding.
A sense of foreboding surrounds Smallville as Clark must choose between staying with Lana and his family or fulfilling his destiny to rule the Earth. Lex and Helen prepare for their marriage, and Chloe considers Lionel's offer to investigate Clark.