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Sue Dibny, wife of the Elongated Man, is murdered, her body horribly burned. The super-hero community rallies to find the murderer.
Early suspicion rests on Doctor Light, as it is revealed that he had raped Sue Dibny years earlier in the Justice League satellite headquarters. It is also revealed that the Atom, Black Canary, Hawkman, Flash (Barry Allen), Green Lantern (Hal Jordan), and Green Arrow allowed the sorceress Zatanna to mind-wipe the captured Doctor Light. Not only was his memory of the rape of Dibny removed, but his personality was also altered to make him less of a threat. Thinking that Light may now have murdered Sue, the superheroes attempt to capture him. However, Light has hired Deathstroke to protect him, and in the ensuing fight between Deathstroke and the JLA, Doctor Light regains his memory, is enraged at the violation, and escapes.
The murderer next tries to hang Jean Loring, the ex-wife of the Atom. The attempt fails. The murderer then sends a death threat to Lois Lane (Superman's wife). Finally, a hit is arranged by Captain Boomerang on Jack Drake, the father of Robin (Tim Drake). However, Jack Drake receives a note warning him of the impending attempt on his life, as well as a gun, both sent by an unknown party. As Jack Drake fatally shoots Captain Boomerang, the latter manages to throw a razor boomerang at Drake's chest, injuring him fatally. Batman confiscates the note before the authorities or the media can learn of its existence.
As the investigation continues, Firestorm (Ronnie Raymond) is stabbed by the Shadow Thief, who wields the Shining Knight's enchanted sword, breaching his skin. Approaching critical mass, Firestorm flies into the sky and explodes.
Bolt is seriously injured in a shootout by two thugs transporting Lex Luthor's battlesuit.
Green Arrow (Oliver Queen) reveals to the Flash (Wally West) that Batman had walked in on the heroes while Zatanna was performing the mind-wipe of Doctor Light. When Batman tried to prevent them from doing so, he was mind-wiped as well.
Eventually, the autopsy of Sue Dibny's body by Doctor Mid-Nite and Mister Terrific reveals that Sue Dibny had been killed by an infarction in her brain. A microscopic scan of Dibny's brain shockingly reveals two tiny footprints as the cause of the infarction.
Mid-Nite and Terrific, along with Batman, separately realize that Sue was murdered by someone with access to the technology of the Atom, Ray Palmer. (Palmer's technology grants him the ability to shrink himself to subatomic size). Before they can discover whether it was Palmer or someone using his technology, Palmer learns that his estranged wife, Jean Loring, is aware of the note sent to Jack Drake (knowledge of which had been kept secret). He deduces that she was the killer.
Loring asserts that she did not mean to kill Sue, nor was it her intention for Jack Drake to be killed. She argues that she sent the note and gun in order for him to protect himself and survive the attack. She tells Palmer that she undertook the plan, which included faking the attempt on her own life, in order to bring Ray back into her life. Palmer realizes that she is insane, and Loring is committed to Arkham Asylum.