A man named Sylvester Pemberton tracks down Chloe and tells her he knows about her team of superheroes and needs their help. However, before he can explain who he is, he is attacked and killed by Icicle. Clark and Chloe's investigation leads Clark to the former headquarters of the Justice Society of America where he meets up with Nelson AKA Dr. Fate, Carter Hall AKA Hawkman and Courtney AKA Star Girl. Courtney pleads with Hawkman and Dr. Fate to help her catch the killer that is targeting their group but they are reluctant to resume their duties as superheroes. Clark, John Jones, Green Arrow, and Chloe team up to help the JSA stop Icicle before he murders another member of the group. Meanwhile, Lois receives a package from a mysterious agency called Checkmate, run by Amanda Waller.
Oliver's past comes back to haunt him in the form of the Dark Archer, Oliver's former teacher, who seeks revenge on his student by taking aim at Lois and Chloe. Oliver faces down The Dark Archer after his former mentor kidnaps Mia AKA "Speedy" but is pushed to his limit and Clark races to stop him from making another deadly mistake.
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.
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.
Jor-El mysteriously arrives at the Kent farm searching for his son, Kal-El, but meets Chloe instead. 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
Oliver tries to help a young street girl, Mia AKA Speedy, get out of her dangerous life by offering to train her, but Mia double crosses him. Lois asks Clark to help her land a job as an on-air television host, but the two are shocked when the station wants to hire them as a team.
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.
Tess forces Oliver to come to a Queen Industries gala to put the Board at ease, but things go awry when the Toyman shows up with a bomb and a plan to take revenge on Oliver. The Toyman tells Oliver he must confess to murdering Lex or he will blow the place up. Meanwhile, as part of his training, Jor-El gives Clark the ability to hear other people’s thoughts.
Zod and his soldiers release a virus into the air that turns humans into zombies. The only way to stop it is to make an antidote from the blood of another Kryptonian. After Lois is infected, Chloe pleads with Clark to donate his blood to stop the epidemic, even though it risks outing him to Zod.
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 kill the vigilante. However, the situation becomes even more complicated when Lois' own investigation leads her into Corben's hands.
