Season two opens with the dust still settling in Smallville following the shocking outcome of the confrontation between Tal-Rho and Superman. 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.

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.