When a doctor that the Kandorians resurrected for experimentation becomes determined to prove that aliens have invaded Earth, he kidnaps several of Zod's people and Lois in the hopes of exposing the truth. Zod disguises himself as a Daily Planet reporter, but is shot during his efforts.
When Clark is exposed to gemstone kryptonite on Valentine's Day, he unwittingly gains the ability to make wishes come true... and chaos results as Lois agrees to have a traditional relationship, and Chloe vows to watch out over Clark and protect him from Lois.
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Zatanna goes to a comic book convention to find an enchanted comic book and asks Clark for his help. While Lois sees them together and becomes jealous, Chloe is rescued from an accident by a teenager who has acquired the comic book and used it to become Warrior Angel.
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A man named Sylvester asks Chloe for help but ends up getting attacked and killed. Clark is led to the former headquarters of the Justice Society of America where he meets up with Dr. Fate, Hawkman, and Stargirl. Later, Clark, John Jones, Green Arrow, and Chloe team up to help the JSA stop the killer before he murders someone else in the group. Meanwhile, Lois receives a package from a mysterious agency called Checkmate.
Oliver's former mentor, the Dark Archer, seeks revenge on his pupil and launches attacks on Chloe, Lois, and Mia as part of his plan. When Oliver is driven to his limits and beyond, Clark must come to the aid of his friend.
Tess takes steps to learn what Lois saw in the future: a powerless Clark subservient to Zod, and Chloe and Oliver leading a resistance group against the Kandorians.
Zan and Jayna come to Metropolis and assist the Blur with his fight to take down crime but several of their rescue attempts fail, which leads Clark in trouble with the District Attorney.
It's a race against time to find Jor-El when Clark realizes that he is on Earth and Zod realizes that he could hold the key to their powers. Chloe is the first to meet him, while Zod enlists Tess.
Oliver offers to train a new girl, Mia, to keep her safe from danger. Lois and Clark are stunned when a TV morning show wants both of them to be their new hosts.
A woman forces Oliver to play in a dangerous game and then turns up dead. The police believe Oliver is responsible and arrest him. Meanwhile, Lois confronts Clark over his knowledge about Oliver's suicide attempt.
The Toyman seeks revenge on Oliver. Clark is gifted the power to hear people's thoughts as part of his training by his father.
A virus spreads through Metropolis that transforms humans into zombies. Chloe and Dr. Hamilton learn that Clark's blood can provide a cure. Meanwhile, Oliver turns to the dark side and must decide the future of his Green Arrow identity, while Tess tries to locate Zod and his Kandorian soldiers.
Lois' new colleague, John Corben, undergoes a horrific transformation when he awakens from an accident with superhuman strength and a heart made of kryptonite. Determined to use his new power to further his vendetta against the Blur, Corben sets out to kill the vigilante. However, the situation becomes even more complicated when Lois' own investigation leads her into Corben's hands.
Clark decides that he is ready to start his training at the Fortress, but Jor-El insists that he return to Metropolis to cut his ties with Lois before he begins. Lois reappears in the city with no recollection of vanishing, and her investigation into a monorail crash brings her into contact with a new reporter named John Corben... who is opposed to the Red and Blue Blur. Meanwhile, Chloe's friendship with Clark deteriorates when he refuses to use the Legion ring to save Jimmy; Oliver turns down a dark path, and Zod makes his entrance at the Luthor mansion.
