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.

Zod unleashes his army upon the world, forcing Chloe to call in reinforcements from old friends. Zod tells Lois he is The Blur and asks her to steal the Book of Rao from Clark. Torn between Clark and The Blur, Lois asks Clark to come clean with her about everything but he refuses. Chloe and Oliver attempt to reconnect Watchtower's satellite system in order to fight the Kandorians but to Chloe's horror, Oliver gets caught on site and disappears. Tess attempts to stop Zod but he leaves her clinging to life. Clark and Zod battle for control of Earth.