Complicating the already daunting job of raising two boys, Clark and Lois must also concern themselves with whether or not their sons Jonathan and Jordan could inherit their father’s Kryptonian superpowers as they grow older. Returning to Smallville to handle some Kent family business, Clark and Lois are reacquainted with Lana Lang, a local loan officer who also happens to be Clark’s first love, and her Fire Chief husband Kyle Cushing. Meanwhile, Superman and Lois’ return to idyllic Smallville is set to be upended when both a mysterious stranger and impassioned self-made mogul Morgan Edge enter their lives.

As Smallville celebrates its first Harvest Festival since Martha’s passing, Clark is reminded what his mother meant to him and learns a lesson that will help him move past her death. Meanwhile, Lois makes a breakthrough in the investigation of Morgan Edge. Lastly, Kyle tries to reconnect with Lana, but it seems like he might be falling back into his old ways.

Lois is worried about Jordan as he and Sarah continue to grow closer. Meanwhile, Clark pays Lana a visit. Lastly, Jonathan has been spending more and more time with John Henry.

Superman's worst nightmare comes to life and Lois confronts Leslie Larr. Meanwhile, Lana, Kyle and Sarah agree to stay to help General Lane.

Lois and Clark struggle as a couple while Chrissy adjusts to running The Smallville Gazette with Lois. Jonathan faces new challenges on the football field, and secrets threaten to destroy Jordan and Sarah's growing relationship. Meanwhile, Kyle grows concerned over Lana's involvement with a new mayoral candidate. Lastly, John Henry Irons and his daughter Natalie attempt to make this new Earth their home.

Clark opens up to Lois about his ongoing struggle with visions and admits that there is only one person who might be able to help. Meanwhile, Lana receives some unexpected news and tensions begin to rise between Lois and Chrissy. Lastly, Sarah breaks plans with Jordan to spend time with Natalie.

Lois reaches out to Ret. General Lane as Clark's visions become worse during heated arguments with both Jonathan and Jordan. Meanwhile, Lana shares her frustrations with Kyle. Lastly, Natalie learns that her father didn't follow through on a promise he made to her.

Superman pleads with Lt. Anderson to investigate Ally Allston and Lois receives some very upsetting news. Meanwhile, Lois helps Lana prepare to fight the good fight. Lastly, Jordan is still irritated with Jonathan for lying to him.

Lois thanks Lana for sticking up for Jonathan when one of the football players mother's starts dogging him for getting football season cancelled. Meanwhile, Jordan's unexpected departure on the mayoral election day leaves Sarah rattled. Lastly, Natalie and Sarah wonder if they notice a spark between John Henry and Lana.

A weary Lois holds vigil at Superman's bedside. Meanwhile, Jonathan and Jordan continue to worry about their father who seems more human now than ever. Lastly, John Henry and Natalie work together to figure out the best way to defend against Ally Allston's powers.

Chrissy Beppo, with the authorization of the Department of Defense, has a message for the people of Smallville, not only is the merging of planets real, it is happening.

An undercover assignment reveals a deadly foe that promises to change the Kent family forever; John Henry is haunted by his doppelgänger's past; Sarah explores what the future holds for her and Jordan; Gen. Samuel Lane reclaims his post.

Lois interrupts an intense conversation between Clark and John Henry. Meanwhile, Kyle tries to run interference between Sarah and Lana. Lastly, Jonathan has a heated discussion with Candice's dad.

Superman and John Henry clash over how to handle Bruno Mannheim, while Lois worries over upcoming treatments and confides in Lana about her early courtship with Clark. Meanwhile, Jonathan, Jordan, and Sarah work together to help Natalie deal with the aftermath of meeting Matteo's family.