This is the plot for Identity Crisis.
(WARNING! THIS CONTAINS MAJOR SPOILERS, READ AT OWN RISK!)
Sue Dibny, the wife of superhero Elongated Man, is murdered in their apartment, apparently dying of burns (the Elongated Man was at the time on a stakeout), The DC superhero community rallies to find the murderer, with villain Doctor Light being the prime suspect. Green Arrow reveals to the Flash (Wally West) and Green Lantern (Kyle Rayner) that Light once raped Sue Dibny in the JLA satellite headquarters. To ensure this could not happen again, the current members of the League - Atom (Ray Palmer); Black Canary; Hawkman; Green Lantern (Hal Jordan) and a very reluctant Flash (Barry Allen) allowed the sorceress Zatanna to mind-wipe the villain and alter his personality.
Further discussion reveals that a mind wipe was also done on another occasion: when the Secret Society of Super Villains (The Wizard; Floronic Man; Star Sapphire; Reverse-Flash and Blockbuster) captures JLA members Superman; Batman; Green Lantern (Hal Jordan); Zatanna and Wonder Woman switched bodies with the heroes, allowing the villains to learn their secret identities. Although the heroes defeat the villains, Zatanna once again erases the villains' memories of the incident, and their knowledge of the secret identities.
The heroes locate Light, who has hired the mercenary Deathstroke to protect him. During the battle Light regains his memory, and enraged by the violation, uses his formerly lost powers to escape. Although questioned by Superman, Wally West continues to protect the heroes and their secret. Jean Loring, ex-wife of the Atom, is found by the hero hanging from a door and he revives her just in time. A death threat is then sent to Lois Lane, (Superman's wife). Flash Rogues gallery villain Captain Boomerang (Digger Harkness) is hired by third-rate villain The Calculator (on behalf of the real killer) to assassinate Jack Drake, father of the current Robin, Tim Drake. Drake, however, receives a gun and a note warning him of the impending attempt on his life. The character fatally shoots Boomerang, but not before the villain throws a razor boomerang into Drake's chest, killing him. Tim Drake discovers the body and is comforted by partner Batman, who confiscates the note before the authorities or the media can learn of its existence.
During the questioning of several villains by the heroes, former League member Firestorm (Ronnie Raymond) is stabbed through the chest with the sword of the Shining Knight by the villain the Shadow Thief. Firestorm' nuclear powers reach critical mass and he detonates in the atmosphere.
Wally West questions Green Arrow again when he accidentally saw a snapshot of the battle on the Satellite in Light's mind, which reveals that Batman was also present. Green Arrow confesses that Batman disapproved of the attempted mind-wipe and also had his memory of the incident removed. Batman uses his detective skills to find the hideout of the Calculator, but discovers the villain anticipated this and abandoned it.
The autopsy of Sue Dibny's body by Doctor Mid-Nite and Mister Terrific - members of the Justice Society—reveals Dibny was killed by an infarction in her brain. A microscopic scan of Dibny's brain reveals tiny footprints as a clue to the cause of the infarction.
Mid-Nite and Terrific realize—as does Batman in the course of his own investigation—that Dibny was murdered by an assassin with access to the shrinking technology of the Atom (the technology allows the ability to shrink to subatomic size). Almost simultaneously Palmer learns that his estranged wife, Jean Loring, is aware of the note sent to Jack Drake (which had been kept secret) and deduces she is the killer. Loring claims she did not mean to kill Sue, and it was not her intention for Jack Drake to be killed, arguing that she sent the note and gun so he can protect himself. Loring states that she undertook the plan (included faking the attempt on her own life) in order to bring Ray back into her life. Palmer says that she is insane, and Loring is committed to Arkham Asylum and kept under heavy medication. The story depicts a final scene with the Justice League:Wally West is awkward in the presence of Batman, who is suspicious of his behaviour.
The ramifications are depicted in the title Flash, as the hero's Rogues bands together at the funeral of Boomerang, and the title JLA, which features a storyline revealing that Batman has guessed the truth.
Captain Marvel/ Brandon Molale
Green Arrow/ Justin Hartley
Zatanna/ Phoebe Cates
Batman/ Christian Bale
Vixen/ Halle Berry
Hawkman/ Michael Fassbender
Martha Kent/ Kathy Bates
Firestorm/ Jensen Ackles
The Atom (Ray Palmer)/ Josh Hartnett
Jack Drake (Robin's father)/ Michael Douglas
Lois Lane/ Erica Durance
Perry White/ Elliott Gould
Jimmy Olsen/ Aaron Ashmore
The Flash (Wally West)/ Taylor Handley
Jean Loring (the Atom's wife)/ Jordana Brewster
Starfire/ Alessandra Ambrosio
Ion (Kyle Rayner)/ Matthew Bomer
IDENTITY CRISIS FAN CAST part 3...coming soon