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, an underground team of superheros, 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 the shadowy Amanda Waller.

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.

Oliver tracks down his tormentor Rick Flag, learns he exchanged him for Chloe, who died poisoned, and informs Clark, who helps him work out Chloe actually staged her fake death. On her Daily Planet assignment in Egypt, Lois meets archaeologist Carter Hall ans soon suspects his story about a reincarnated Pharaonic prince is autobiographic. Clark dislikes her staff replacement Cat Grant, but saves her from never identified, yet infallible assassin Deadshot and learns he was the actual target, actually hired by Flag, knowing Superman's weakness is his noble need to protect.

As the VRA threat intensifies, Clark takes initiative by closing down watchtower and declaring the League go officially underground, but will this be enough to stop Lt.Trotter and Slade Wilson aka Deathstroke from exposing them? Tensions rise in this mid-season finale.