Clark Kent and Lois Lane's family life is complicated when they are forced to bring their teenage sons to Smallville, where truths are forced out into the open – while a mysterious foe attempts to draw out Superman to kill him.
Clark's efforts to teach Jordan about his family history and his new powers are complicated by the stranger who has targeted Superman for revenge. Lois decides to take on Morgan Edge with an article for the Daily Planet, and Jonathan is frustrated by his efforts to join the football team.
Jordan decides to stand up to his bullies by joining the football team, while Lana clashes with her increasingly distant daughter. Lois and Chrissy meet a source with new information about Morgan Edge, leading to a disturbing confrontation.
With billionaire Morgan Edge in town to drum up support for his plans, Lois plans to public a scathing exposé of her former boss. General Sam Lane monitors a prisoner transfer, putting Clark between his job as a hero and as a father.
The Kent family's first Smallville Harvest Festival is disrupted by the return of a missing man. John is caught off guard by his girlfriend back in Metropolis, and a stranger approaches Lois.
Jordan is attacked by a super-powered student from his high school, who is on the run from General Lane and the D.O.D. The Crows travel to Metropolis for a big football game, and Lois finds an unexpected ally in her efforts to infiltrate the town mine and discover Morgan Edge's secret.
Lois and Clark pursue Edge's shipment of X-Kryptonite, only to find that their mysterious new ally has beat them to it – someone who has a connection to Lex Luthor. Meanwhile Jordan struggles to control his new super hearing.
Clark and Lois discover that John Henry Irons is from a parallel world where Superman was a villain. Lois struggles with a very personal parenting crisis, and Sarah's dad tries to convince her to audition for the school's musical review.
Morgan Edge's experiments in creating artificial Kryptonians turn to Lana's co-worker Emily. After Clark displays lingering symptoms of the D.O.D.'s aerosolized kryptonite, Jordan falls dangerously ill.
After learning about Edge's plan to resurrect Krypton, Superman and his allies seek a way to restore the residents who have been transformed. Meanwhile Lana looks for an explanation for Kyle's strange behavior.
While recovering at the Fortress Superman recalls his past, from his training with Jor-El to his early days working alongside Lois at the Daily Planet. But Morgan Edge has his own sinister agenda for Clark's future.
Lois turns to John Henry Irons after Superman is taken by Morgan Edge, only to be forced to try and convince him not to kill her husband. Kyle finds it difficult to return to his normal life, and Jonathan encourages Jordan to work on strengthening his powers.
With Tal-Rho in custody and his ally Leslie Larr on the run, Superman and his family debate whether the D.O.D. should eliminate its anti-Kryptonian weapons. The Cushings are distraught by the town having turned against them, and Chrissy clashes with Lois when she gets too close to her own story.
With the town in an upheaval over the D.O.D.'s continued presence in Smallville, Lois tries to mediate -- knowing that Edge still poses a grave threat to the town. Clark learns that Lana and Kyle are considering leaving town.
Jordan is abducted by Tal-Rho, who plans to use him for his father's endgame to resurrect Krypton – forcing Superman to face off with his own son for the future of Earth.
