It's been four weeks since the Fortress collapsed and Clark disappeared. Green Arrow calls upon Black Canary and Aquaman to locate the missing Clark Kent. Clark, in the meantime, is powerless and residing in a Russian prison camp in Siberia. With Lex Luthor missing and presumed dead, a new ruthless CEO, named Tess Mercer, is appointed the head of LuthorCorp and moves into Lex's mansion with her own dark plans for Clark and Metropolis. Chloe is kidnapped by a clandestine group that has discovered her special powers and they want to test the limits of those new powers by locating Green Arrow and his friends.

Clark's first day on the job at the Daily Planet begins with a bus exploding right outside the building, which leads him and Lois on a trail of someone who might be infected by kryptonite. Chloe finds a runaway teenage girl, named Bette, whom Chloe suspects is involved in the explosion when Bette (whom will later become the fire-starter Plastique) has the meteor-rock power of pyrokinesis. In the meantime, Chloe also meets a local medic, named Davis Bloom, who takes an interest in her, even though she's engaged to Jimmy Olsen. Elsewhere, Tess meets Clark for the first time as she takes over the Daily Planet in Lex's absence and immediately senses something not right about him.