Crisis Of Conscience was the first story to directly tackle the consequences of the Justice League’s actions in IDENTITY CRISIS and was published in JLA #115 to #119.
JLA #115 The Flash collects the members of the League who took part in the mindwiping of Dr Light after he had attacked Sue Dibny. They explain to the Martian Manhunter, who had not been party to the act, that the Secret Society of Supervillains had once learned the Leaguers’ identities and, after catching them, Zatanna had wiped their memories. When Batman found the League doing the same to Dr Light, they wiped Batman’s memory and hid their own from Manhunter in case he accidentally found out.
As they discuss how to confess their actions to Batman, they receive distress calls from former League members and, upon answering them, find them attacked by members of the old Secret Society of Supervillains. Overcoming the Leaguers, the Society transports them to Gotham where they find Batman, Martian Manhunter and Catwoman. They reveal their memories have been restored and they remember the identities of the Leaguers.
JLA #116 The League battle the Society who reveal they have a mysterious benefactor who has restored their memories; once a stand-off is reached, the Society vanish. The League journey to the Batcave determined to apologise for their actions in wiping Batman’s memory. Things come to a head as Batman lashes out at the League, spurning their apology, forcing them to leave the cave and return to their loved ones. Martian Manhunter returns to the Watchtower and finds the benefactor of the Society to be Despero.
JLA #117 The Martian Manhunter and Despero battle each other as they have so many times before. The Society, meanwhile, attack the Daily Planet building in Metropolis, targeting the loved ones of the League members, in this case Superman’s wife Lois Lane. The League arrive along with Superman and defeat the Society but not before several of their members refer to Superman as either Clark or Mr Kent. With the Society captured, Superman reveals that he knew the League had previously wiped their minds though he didn’t agree with it; when asked what to do with the fact that the Society know their identities again, Hawkman demands they vote to mindwipe them once more.
JLA #118 Despero and the Martian Manhunter’s battle comes to Earth where Aquaman steps in to help his friend. In Metropolis, Hawkman outlines his plan to remove just the knowledge of the League’s identities from the Society members’ minds and they vote but Zatanna, who has the deciding vote, elects to quit the League instead of wiping anyone’s mind again. She retires to Paradise Island and speaks with Wonder Woman who had recently killed Maxwell Lord in the Sacrifice story; Wonder Woman tells her that, though she may not want to, Zatanna may need to use her powers to wipe the Society’s minds. The League return to the devastated Watchtower in order to find Martian Manhunter to ask him what to do about the Society. Despero, meanwhile, has taking over both Aquaman and Manhunter and attack Batman and Catwoman in the Batcave, taking control of Batman too.
JLA #119 The League answers Catwoman’s emergency signal and battle Despero and the mind controlled Leaguers. More and more of the League fall under Despero’s control until Zatanna appears, using her magic to halt Despero’s rampage and restore the League’s minds. Realisation dawns, however, that the League itself is splintered and falling apart and if comes down to the Martian Manhunter to rebuild it as he had done previously. Zatanna accepts her responsibility to protect her friends and their loved ones and removes the knowledge of the League’s identities from the Secret Society members. The Martian Manhunter returns to the Watchtower where he is attacked by an unknown assailant and the Watchtower destroyed, leading directly into INFINITE CRISIS #1.