After Jodi Keenan, the wife of a Special Forces soldier, sets off a pipe bomb in one of Lex's secret labs, Lionel is severely injured and Lex is taken hostage by the enraged spouse. Claiming Lex kidnapped her missing husband, Jodi threatens to blow up the entire lab with Lex inside unless he tells her where her husband is. Lex naturally denies knowing Jodi's husband, Wes, Clark sets off to rescue Lex, but is immediately felled by the kryptonite lining the earthen walls. Lex and Clark realize the only way they will make it out alive is by helping each other before the bomb detonates. Meanwhile, Lionel reveals to Lana why he forced her into marrying Lex, which leads her to investigate Lex's secret research of his 'Project 33.1' research as well as his work in tracking down the Phantom Zone escapees to capture and use one as part to create his army of 'super-human' soldiers.

Clark and Lois discover Kara's spaceship but before they can open it, Kara appears and knocks Lois out. Clark is shocked after Kara tells him she is there to protect baby Kal-El. Despite Kara's appearance, a despondent Clark decides that without Lana there is nothing keeping him in Smallville, and heads to the Fortress of Solitude to begin his training as a superhero. However, Jor-El tells him Kara's father- Zor-El, who is Jor-El's brother- is evil and Kara is dangerous, therefore Clark must stay in Smallville to find out why she came to Earth. Lex makes a stunning discovery regarding Lana and Project 33.1.

Oliver Queen is poisoned at a charity fundraiser and Clark races around the world to find a cure.

A man named Sylvester Pemberton tracks down Chloe and tells her he knows about her team of superheroes and needs their help. However, before he can explain who he is, he is attacked and killed by Icicle. Clark and Chloe's investigation leads Clark to the former headquarters of the Justice Society of America, an underground team of superheros, where he meets up with Nelson (AKA: Dr. Fate), Carter Hall (AKA: Hawkman) and Courtney (AKA: Star Girl). Courtney pleads with Hawkman and Dr. Fate to help her catch the killer that is targeting their group but they are reluctant to resume their duties as superheroes. Clark, John Jones, Green Arrow and Chloe team up to help the JSA stop Icicle before he murders another member of the group. Meanwhile, Lois receives a package from a mysterious agency called Checkmate, run by the shadowy Amanda Waller.

Zod continues to pose as "The Blur" and asks Lois to investigate one of Tess' secret labs. An explosion rocks the lab, and Lois is rescued by John Corben who was a subject of multiple experiments. While investigating the explosion, Clark is exposed to red kryptonite. And infected Clark takes Zod to the Fortress. Tess turns to Chloe for help and they send in Corben to stop Clark from revealing all his secrets.