In all further references to the JLA's pre-Crisis adventures, including its origin story and the Secret Society incident, Wonder Woman is replaced by Black Canary.

Following the death of Elongated Man's wife Sue Dibny, the superhero community rallies to find the murderer, with recurring villain Doctor Light being the prime suspect.

Further discussion reveals that a mind wipe was also done on at least one other occasion to prevent the Secret Society of Super Villains (the Wizard, Floronic Man, Star Sapphire, Reverse-Flash, and Blockbuster) from retaining their knowledge of League members Superman, Batman, Flash, Green Lantern (Hal Jordan), Zatanna, and Black Canary.

Atom finds his estranged ex-wife Jean Loring hanging from a door, blindfolded and gagged, and revives her just in time, but she is unable to describe her attacker.

The autopsy of Sue Dibny's body by Doctor Mid-Nite and Mister Terrific, members of the Justice Society, reveals that she was killed by an infarction in her brain caused by an unidentified microscopic person.

Batman, Mid-Nite, and Terrific realize that Sue was murdered by someone who has access to Ray Palmer's technology, which as the Atom, he uses to shrink himself to subatomic size.

[5] It is revealed in that storyline that the Justice League's mind manipulation, Jean Loring's turn to villainy, and Sue Dibny's rape by Dr. Light were three of the many indirect changes effected by Alexander Luthor Jr. and Superboy-Prime when they caused overlaps of parallel timelines (Hypertime) from their pocket universe since after the events of Crisis on Infinite Earths.

[6] The miniseries was selected by the Young Adult Library Services Association (YALSA)'s 2007 recommended list of Great Graphic Novels for Teens.

Sims' colleague, Matt D. Wilson, did not concur with that exact assessment, but felt that the miniseries did a disservice to its protagonists: "Virtually every hero comes out of Identity Crisis looking like a jerk, a victim or a pariah".

[10] Dominic Organ, writing for Comics Bulletin, was critical of the series' artwork, stating it was "incredibly spotty in places", inconsistent and "at times it is downright ugly".