Clark teams up with Zod's wife, Faora, to investigate the abduction of her sister, Vala, and several Kandorians whom have been experimenting with humans in order to find a way to claim their super powers, while Lois herself is abducted by Bernard Chisholm, a former doctor the Kandorians experimented on, claiming that there are aliens on Earth and he wants the skeptic Lois to write an article about it. But when Zod goes off on his own and tries to stop Chisholm, without his super powers, Clark is conflicted whether to save the life of his enemy. Meanwhile, Oliver investigates the disappearance of money from Tess' company accounts and he discovers that Chloe is responsible and using the embezzled money to construction Kryptonite weapons for possible use against Zod and the Kandorians.

Tess's latest intrusion, at Watchtower, and Chloe's excessive lockout mechanism, lock the pair up, likely to be killed while Checkmate breaks trough the last firewalls. Intrudening the Luthor mansion Oliver faces Zod, whose abusive side reemerges, now with superpowers. Clark must save his friends and hopes to do he same for the Kandorians, one of which carries unsuspecting Zod's unborn child, but the all-round secrecy exacts terrible prices.

Clark is desperate to find the Book of Rao before Zod can find it. If it falls into Zod's hands, he will take over Earth. He's asking Chloe for her help. She is hampered by Tess's ravaging of her Watchtower equipment. Lois tells Clark she has a sure-fire way of getting their jobs back, but he is too preoccupied to listen. Her feelings are hurt. She says she needs a mission in life. In the midst of all this, Clark's mom returns unexpectedly with Perry White, whom she has been dating. Lois is smitten with Perry and shows him her hot lead - a photo of the Red/Blue Blur and tales of an alien race that is looking for the Book of Rao. She holds up a picture of it. Perry's jaw drops. He reaches into his briefcase and pulls out a copy of the same symbol. He tells her that they have a shared story. He is investigating an explosion of a secret government complex in the Rocky Mountains but has been blocked by someone with the code name, Red Queen. Meanwhile, Maxwell Lord has imprisoned Tess, demanding that she hand over the Book of Rao. As Chloe tries to help Clark search for the book, the Red Queen locks her computers. At an uncomfortable "family" dinner, Lois informs Clark that she's breaking up with him. Tess awakes from the mind manipulation that Lord has been using on her to get the Book of Rao. She grabs his gun and escapes. She heads home to get Rao from her wine cellar hiding place. But the real Red Queen - Martha Kent - holds her at gunpoint, knowing she would go for Rao when she fled Lord. Tess is forced to hand it over. Perry and Lois's story collapses, but his good word to the Planet editor gets Lois and Clark their desks back. At the Kent farm, Clark tells his mom that he knows now she is the Red Queen. She answers back that she has never stopped trying to protect him. If he uses the knowledge in the Book of Rao to exile all Kryptonians to another plane, it will exile all Kryptonians from Earth, including himself. She hands the Book of Rao to him.

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.