On Apokolips, Darkseid orders his agent Lady Death to await his orders on the dark side of the Moon. The Phantom Stranger arrives, noting that Darkseid created the new Secret Society of Super-Villains to occupy Captain Comet's Rehab Squad and a new Injustice Gang to occupy the JLA. Darkseid instructs Lady Death to target Smallville. Lady Death lands in Smallville, claiming the planet for Darkseid. Superman arrives, spotting Lana Lang in the crowd of onlookers, and battles Lady Death, who has the power of a Kryptonian. After their battle takes them into the Superboy Museum, Lady Death introduces herself, and Superman is forced to let her go after being exposed to a kryptonite ring from an exhibit. Lana Lang, having come home after Morgan Edge fired her from WGBS, saves Superman's life. Lana uses this story in order to win her old job back. Superman contacts the JLA for help, but the team is still cleaning up after Despero, and the Flash II and Zatanna are investigating rumors of the new Injustice Gang. Following Lady Death, Superman sees her fly into the time stream, and the Phantom Stranger arrives to tell her she has traveled to the future of the 30th century. [“Superman: The Apokolips Factor, Chapter 1: Lady Death”]
In the 30th century, three days after Saturn Girl and Lightning Lad leave Earth to stay on Winath, the Legion of Super-Heroes is discussing the events of the Crisis when Lady Death appears in Metropolis and wreaks havoc. Superman arrives to help. The future version of Darkseid vows to send Lady Death back to the past to meet her destiny. Lady Death defeats Ultra Boy, and the Legionnaires wonder who she is. The Phantom Stranger arrives and offers only an enigmatic clue of her identity. After Lady Death breaks into LSH Headquarters, she attempts to kill Brainiac 5 but cannot do it. Just then, a Boom Tube created by Darkseid appears and takes Lady Death away. The Phantom Stranger says Superman has failed to prevent this occurrence and must return to the past to repair the damage. [“Superman: The Apokolips Factor, Chapter 2: The Sands of Time”]
Returning to the 20th century, Superman realizes that Lady Death arrived while telepathic heroes were busy – she first appeared at a time when both Captain Comet and the Martian Manhunter were occupied with the Secret Society of Super-Villains and the Injustice League, respectively, and she had arrived in the 30th century three days after Saturn Girl's retirement. Arriving in Smallville in his own time, Superman is surprised but pleased to see the arrival of several members of the Justice Society of America of Earth-Two – Doctor Fate, the Spectre, Power Girl, the Flash, and the Star-Spangled Kid. Superman and the JSA travel to Apokolips, where they encounter Darkseid, Mantis, and Lady Death. Superman and the JSA battle Lady Death and the parademons, until Lady Death's helmet falls off, and Superman recognizes her. Elsewhere, the Spectre is revealed to be Tannarak when he appears at the lair of Prof. Ivo, who had created super-powered android lookalikes of four JSA members. The Phantom Stranger is revealed to be behind the deception in order to provide assistance to Superman, having freed Tannarak and gained Ivo's help, but he is forbidden to reveal the deception as part of their agreement. [“Superman: The Apokolips Factor, Chapter 3: Legends”]
Superman and the false JSA are shocked to learn that Lady Death looks exactly like Kara Zor-El (Supergirl) and speaks Kryptonian. Tannarak disguised as the Phantom Stranger arrives and brings Superman, Lady Death, and the false JSAers with him back to Smallville. There, he tells Lady Death that the Phantom Zone villains have been set free. The false Stranger explains that Darkseid, noting the Monitor's satellite over Earth-One, realized that the Crisis was coming and wanted an agent on Earth. He attempted to clone Superman but failed and turned to a Phantom Zone villain – General Dru-Zod, who once used an army of imperfect clones to attempt to conquer Krypton (General Zod's original clones were too perfect and refused to follow his orders, so he adjusted his matrix to create Bizarro-like clones instead that were obedient to him), and was sent to the Phantom Zone for it. But when Zod escaped with the other Phantom Zone villains, Superman was sent into the Phantom Zone, so instead Darkseid used Zod's cloning matrix to clone Supergirl, supposedly replacing the real Supergirl a few months later, and that it was this cloned Supergirl who died in the Crisis. Darkseid remotely activates an explosive on Lady Death, and Superman throws it outside of the atmosphere, where it explodes with a force beyond Earth's nuclear potential. Upon returning, he finds the false JSA gone, while the real Phantom Stranger has replaced the false one. Lady Death then leaves, and the Stranger stops Superman from following her. Watching, Darkseid knows Lady Death's secret. The shock waves from the detonation pass into the Fifth Dimension, reverberating in the Mxypltk-Aethyr being and threatening to destroy him. Superman contacts J'onn J'onzz at the JLA satellite and tells him his suspicions that the JSAers weren't the real deal. As J'onn wonders why anyone would impersonate the JSA, the real Phantom Stranger arrives with a warning to the JLA about a great evil approaching that may destroy the team from within, and then he vanishes. [“Superman: The Apokolips Factor, Chapter 4: The Phantom Zone Revisited”]