While Clark is still frozen in the fortress, Bizarro grows closer to Lana, who returns the feelings on just as deep a level, even sharing some badly-needed information with him while he still attempts to carry out his intentions of destroying Clark. Lex's brother, Julian, reveals himself to Lionel in an effort to clear the air between all parties involved.
Pete Ross returns to Smallville and finds a number of surprising changes since his departure four years earlier. Besides resolving his feelings toward Clark since he learned of his friend's secret, Pete has to deal with the acquisition of a superpower of his own: that of his ability to 'stretch' his body courtesy of kryptonite-laced gum he's been chewing and consuming for nearly a year. Meanwhile, Lex continues to sow seeds of anxiety into the amnesiac and powerless Kara over Clark as well as wanting to know about her past, as does Jimmy Olsen.
Lionel kidnaps Clark and holds him in a kryptonite-lined cell at a Luthorcorp facility; Chloe and Lana confront Lionel, who blames Lex, and they then take Kara to the Fortress and plead with Jor-El to restore her memory so she can save Clark.
When a member of the Veritas clan attacks in his name and carves Kryptonian symbols in the victim's chest, Clark stands by his principles in hurting no human being, even though the victim is Lex Luthor
Clark feels that Kara is under the effects of red kryptonite when he discovers that she is the reason for the plane containing the last member of the Veritas exploding. Lex is directed to look for answers surrounding the traveler in the Arctic Circle, where Clark's Fortress of Solitude rests.
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 ...
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 pyrokinisis. 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 ...
When Tess inadvertently activates the mysterious Kryptonian Knowledge crystal found in the Artic, it omits a high-band beacon which summons an alien queen, named Maxima, who arrives on Earth and begins a search for her new mate, with a kiss that is too strong for humans to survive. Meanwhile, after just moving in together, Jimmy finds a letter that Chloe wrote for Clark that revives Jimmy's insecurities.
Jimmy takes a photo of Clark using his super-speed while saving Lois from danger, but it comes out blurred. Tess decides the story should make the front page for the Daily Planet exposing the mysterious new 'superhero' that. Chloe refuses to continue helping Clark protect his secret, so Clark turns to Oliver for help when Jimmy gets too close to discovering his secret. Meanwhile, Lois meets Sebastian Kane, a new reporter at the Daily Planet, who has the power to see peoples' memories by merely touching. He has been hired by Tess to find the missing alien crystal.
Clark receives a crystal that sends him and a visiting Lois to the Phantom Zone where they run into Kara. Kara tries to open a portal for Lois before it's too late but Zod's wife, Faora, manages to escape in Lois's body and proceeds to go on a rampage through the streets of Metropolis.
When Chloe begins having memory loss when the essence of Brainac begins replacing her memories with Kryptonian codes, Clark decides to use the Cryrstal of Knowledge to reconstruct the Fortress of Solitude and ask the spirit of Jor-El for help. Meanwhile, Jimmy begins to worry about Chloe's well being, while Davis, disturbed by knowledge that he may have alien origins, begins to become drawn to Chloe.
Oliver gets a step closer to finding Lex, but Clark refuses to help for the time being, due to Chloe's special day, while Lois finds she has special feelings for Clark, who has a surprise (or two) waiting for him at the wedding reception.