Early suspicion rests on Doctor Light, as it is revealed that he had raped Sue Dibny years earlier in the JLA 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. In the ensuing fight between Deathstroke and the JLA, Doctor Light regains his memory, and enraged by the violation, he escapes.
The murderer next tries to hang Jean Loring, the ex-wife of the Atom. The attempt fails, as the Atom arrives in the nick of time and snaps the rope from the inside. The murderer then sends a death threat to Lois Lane (Superman's wife). Finally, a hit is arranged by Captain Boomerang on Jack Drake, Robin's (Tim Drake's) father. 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. Jack Drake fatally shoots Captain Boomerang. Captain Boomerang manages to throw a razor boomerang at Drake's chest, killing him. 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.
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, although in his case Zatanna only removed his memory of the past few minutes.
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 a clue to 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.
Elongated Man - In issue #1, Ralph Dibny is sent on a mystery by his wife, Sue, as part of a gift. He is the first hero to suspect Dr. Light in the murder of his wife. Ralph struggles to maintain a solid form while grieving Sue's death, and is shown in the final scene of the series "speaking" to his deceased wife.
Batman - The Justice League of America's most accomplished detective, Batman plays a major role in solving the mystery of Sue Dibny's murder and Jean Loring's "attempted murder." It is revealed in issue #6 that after he teleported off the satellite to deal with an emergency, Sue was raped by Dr. Light, and that he returned as Zatanna was in the process of altering Dr. Light's personality. He attempted to stop her, but she used a spell to render him motionless. She subsequently removed his memories of the attack. When the JLA battled Dr. Light in Identity Crisis #3, he projected a memory of the JLA, including Batman, restraining him on the satellite following the rape. This led Wally West to deduce that Batman had been present for the incident, and that he had been mindwiped. Batman's eventual remembrance of the mindwipe led him to disassociate himself from the JLA and become increasingly suspicious of metahuman heroes (see Brother Eye).
Hal Jordan - Earth's first Green Lantern responded to Sue Dibny's rape and voted against the alteration of Dr. Light's personality. Hal later became the supernatural Spectre, God's Spirit of Vengeance. Green Arrow consulted him in issue #4 and attempted to get him to exact revenge on Sue's killer in this role. Hal refused, ascribing his acts to a higher purpose, at the same time foreshadowing his return in Green Lantern: Rebirth.
Zatanna - Zatanna responded to Sue Dibny's rape and performed the personality alteration of Dr. Light, as well as the restraint and mindwipe of Batman.
Black Canary - Dinah Lance responded to Sue Dibny's rape and voted against the alteration of Dr. Light's personality.
The Flash - Barry Allen responded to Sue Dibny's rape and was forced into the unenviable role of the deciding vote in the decision to alter Dr. Light's personality. He voted for the mindwipe. In the present day, Wally West figured out that Batman had also been mindwiped and confronted Green Arrow about it. According to Green Arrow, Barry's decision to vote for the mindwipe took place six months after his wife, Iris, was thought to have been killed by Professor Zoom.
The Atom - Ray Palmer responded to Sue Dibny's rape and voted for the alteration of Dr. Light's personality. It was eventually discovered that his ex-wife, Jean Loring, had been responsible for the murder of Sue Dibny and her own "attempted murder". She claimed that by doing so, Ray would feel compelled to get back together with her. He had Jean committed to Arkham Asylum. Immediately afterwards, he discarded his Justice League communicator and shrank himself to a microscopic size. He later appeared talking to his old friend Carter Hall, although he asked for the meeting to remain secret.
Robin - When the mystery killer (later revealed to be Jean Loring) began attacking the loved ones of Justice League members, Tim became especially concerned about his father, who always regretted his son leaving behind a normal life to be a crimefighter. Tim was devastated when Captain Boomerang, hired by the Calculator, who was following the directions to put a cheap hit out by Jean Loring, killed his father. In his final act, Jack killed Boomerang with a gun supplied by Loring.
Deathstroke the Terminator - A hired assassin capable of using 90% of his brain capacity for strategy and reaction during battle, Deathstroke fought the JLA with Dr. Light in issue #3. He defeated most of the JLA before Green Arrow stabs him in his right eye.
Captain Boomerang - A member of the Flash's Rogues gallery, Digger Harkness discovers during the series that he has an illegitimate son originally, but mistakenly, believed to be by Golden Glider who possesses both his own prowess with a boomerang and limited super speed. He is hired by Jean Loring to kill Jack Drake, and succeeds in doing so, but not before he is shot and killed by Drake. His son takes up his namesake and has since joined the Secret Society of Super Villains. After DC's timeline jumped ahead One Year Later, the new Captain Boomerang has joined the superhero group the Outsiders.
Merlyn - A former member of the League of Assassins, Merlyn is the leading voice of the villains, telling the events of the story in counterpoint to Green Arrow, of whom he is an enemy. He is allied with Deadshot and Monocle.
Jean Loring - Once married to the Atom, the accomplished attorney attempted to force a reconciliation with her husband by killing Sue Dibny and targeting the loved ones of JLA members, including Lois Lane and Jack Drake. She murdered Dibny by using one of the Atom's old costumes to shrink down to a microscopic size, break into the Dibnys' apartment, and kill Sue. To attempt to hide the evidence, she badly burned Sue's body. Dr. Mid-Nite and Mister Terrific eventually discover microscopic footprints on Sue's brain tissue and mistakenly suspect the Atom in her murder, but Ray Palmer discovers Jean's true story and has her committed to Arkham Asylum. Later, while still committed, she would be possessed by Eclipso.
The Calculator - Noah Kuttler is a former third-tier villain who has set himself up as an anti-Oracle. He is friends with Captain Boomerang and hires him to kill Jack Drake on behalf of Jean Loring. He has since become a core member of Lex Luthor's Society.
In 2005, DC published several mini-series under the umbrella title Countdown to Infinite Crisis which lead up to the Infinite Crisis limited series. These stories, to an extent, constituted a continuation of Identity Crisis (with further reference to 1985's Crisis on Infinite Earths) and continued in the same vein of controversial storytelling that marked the earlier series.
In Ambush Bug: Year None #1, the plot of Identity Crisis is satirized by Ambush Bug calling Jean and telling her about Sue's party, which Jean had no knowledge of, and Bug stating that Sue made some remarks about Jean behind her back. Bug even suggests to put "a flea in (Sue's) her ear", which Jean said she would do herself. Shortly after, Bug is hunted down by Bat-Girl (Bette Kane), who tells Bug that Sue Dibny was her mother and her father was the Phantom Stranger.
Dominic Organ from Comics Bulletin was critical of the artwork stating it was "incredibly spotty in places" and "at times it is downright ugly". Although he was impressed with some of the artwork especially the panel of Batman racing back to Tim's apartment where he noted "the fear is palpable and all over Batman's face, a single panel that will stick with me for some time I am sure." He praised the story with the stand out being "the human tragedy of it all".