After losing their careers and experiencing a family tragedy, Clark Kent and his wife, Lois Lane, bring their teenage twin children, Jonathan and Jordan, back to Smallville. As he struggles to adapt to life, Clark encounters a mysterious new danger.
Tensions between Lois and Morgan Edge start to grow as Lois and Clark make a crucial decision regarding one of their sons while settling into their new lives in Smallville. The Kent family is invited over for a cookout by Lana Lang Cushing.
At a family breakfast, Clark tells Jordan and Jonathan about his Kryptonian past. In the meantime, Lois and Chrissy investigate further to learn the whole truth about Morgan Edge.
General Lane demands a backup plan against Superman, Morgan intends to build a super-army out of X-Kryptonite, Lois keeps looking into Morgan's dubious activities, and Clark wavers between his responsibilities as Superman and his role as a father.
Luthor attempts to assist Lois as the Harvest Festival approaches in Smallville, a missing Derek returns with newly activated powers, resulting in a violent altercation with Superman, and Jonathan experiences sadness and bitterness because of his relocation to Smallville.
Lois must trust an unlikely ally as she continues her investigation into Morgan Edge, while Clark rethinks his decision to allow Jordan to play football.
Jordan is distressed by the appearing of his superpowers, and Clark finds it difficult to help him. Lois looks into Luthor's true identity and his unexplained whereabouts. Natalie reveals that she is connected to a post-apocalyptic reality in which Earth has been overrun by Superman.
Lois begins therapy with Clark's encouragement after a violent outburst, confronting her lingering grief over a previous miscarriage, and Jonathan finds himself in danger when John Henry's car attempts to kill him, leading to a desperate confrontation between him and Superman.
As Lois, Clark, and Cressie look into Morgan Edge's real motivations, they find that X-Kryptonite is essential to his strategy of using it to target his subjects. Jordan has contracted the same Kryptonite virus that infected his father.
When Kyle starts acting suspiciously, Lana calls Lois and Clark. Superman then uses all of his abilities to liberate the possessed people of Smallville. Sara is furious after confronting her mother about her ongoing cover of Kyle's issues.
After recalling his early days as Superman and meeting Lois, Clark reveals something unexpected about Morgan Edge.
Superman fights Morgan, who is trying to force-implant General Zod's consciousness into him. General Lane recruits John Henry to stop a Zod-possessed Superman. Jordan uses his super-hearing to locate his father.
Jonathan gets a much-needed diversion during a difficult school day, Lois and Chrissie collaborate to create a cover story to protect the Cushings, and Superman stops by Morgan Edge.
As Jordan and Sarah continue to become closer, Lois worries about him. Clark stops by to see Lana. Jonathan's time with John Henry has been increasing.
The darkest nightmare of Superman becomes a reality. Leslie Larr gets confronted by Lois. Sarah, Kyle, and Lana decide to stay in order to support General Lane.