Clark decides that he is ready to start his training at the Fortress of Solitude to become 'Superman'. However, the spirit of Jor-El insists that he return to Metropolis to cut his ties with the people he knows before he begins. Lois reappears in the city with no recollection of vanishing to the future. Her investigation into a monorail crash brings her into contact with a new reporter named John Corben. John is opposed to the "Red and Blue Blur", and has a secret power and identity himself. Meanwhile, Chloe's friendship with Clark deteriorates when he refuses to use the Legion ring to go back in time to save Jimmy. Elsewhere, Oliver turns down a dark path in his quest to rid the world of evil. General Zod makes his entrance at the Luthor mansion before Tess.

Jor-El mysteriously arrives at the Kent farm to hide the Book of Rao, but meets Chloe instead. She tells him that his son, Kal-El is on Earth and lives at the farm. Convinced the Blur is Jor-El, Zod enlists Tess's help in finding him to force him to reveal the secret to his powers. Clark realizes Jor-El is alive and on Earth and races to find him before Zod does.

Tess kidnaps Lois to find out where Lois went after she disappeared for weeks. Lois's memory of the future depicts a Metropolis under Zod's rule and Clark powerless under the red sun, while Chloe forms a resistance group with Oliver. After learning of these future events, Clark makes an important decision about Zod.

Someone with Oliver's skills as an archer take aim at Lois and Chloe.

It is Valentine's Day and while Clark is out on a date with Lois, he unknowingly becomes infected by gemstone kryptonite, which has magical wish-fulfilling properties. Clark mentions to Lois that he wishes they had a more traditional relationship, so Lois quits the Daily Planet, moves in with Clark and starts planning their wedding. Still unaware of his new power, Clark also casually tells Chloe he wishes she would spend more time watching out for him, so an infected Chloe takes his wish to heart and sets her sights on a new target: Lois. Meanwhile, Zod quarrels with Tess as well as his wife, Faora, over the construction of the new solar tower which he hopes will restore his and the Kandorians super powers which will enable them to take over the Earth.

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.