Clark tells Oliver that he must kill Davis, but Clark deals with the fact that he can't take a human life. This leaves the justice league to take the affair on their own hands. Then, Rokk Krinn teleports from the 31st Century to give Clark another Legion time-traveling ring so Clark can exile Davis/Doomsday to the future. But in a surprising twist, Lois confronts Tess about her nefarious plans involving a mysterious crystal and in the fight, Lois accidentally finds Rokk's ring, and gets zapped into the future. Meanwhile, Chloe gets in the middle of Clark and Oliver's fight about Doomsday's human carnage, in which Dianah/Black Cannary and Bart/Impulse intervene. Jimmy finds out Clark's identity, leading to a fateful showdown when Clark attempts to use black kryptonite to split Davis from Doomsday and seal the beast in a large hole in the ground. But nobody is prepared for what Davis will do afterwords.

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.

A mysterious woman forces Oliver to play in a dangerous game of Russian Roulette and then turns up dead. The police believe Oliver is responsible and arrest him, while Clark reluctantly sets out to prove Oliver's innocence. Meanwhile, Lois angrily confronts Clark over his knowledge about Oliver's suicide attempt.

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.

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.