Wally West was shocked by the actions of the JLA in Identity Crisis and then discovered even more dark secrets about Barry Allen in a related Flash story.
Brad Meltzer and Rags Morales’ Identity Crisis was one of the most influential DC comics stories of the 2000’s and remains one of its most controversial to this day. The dark murder mystery drew equal praise and criticism for the massive changes it made to the DC universe and it continued to influence stories in a wide range of series for the rest of the decade until The New 52 reboot. The story began with the brutal murder of Sue Dibny, wife of the Elongated Man, the investigation into which revealed a dark secret within the superhero community. Discovering this secret caused Wally West, a.k.a. The Flash, to question his faith in his beloved predecessor Barry Allen, and Wally’s doubt was only exacerbated when further revelations about how Barry handled one of his most dangerous villains were revealed.
After Sue’s murder, Wally and other heroes discovered that a small sect of the Justice League, including Green Arrow, Black Canary, Green Lantern, Hawkman, the Atom, and Barry (who was the Flash at the time) had used Zatanna’s magic to erase the memories of various supervillains who discovered their secret identities in order to keep their loved ones safe. In Doctor Light’s case, they also modified his personality to make him less of a threat. This had the unintentional effect of essentially lobotomizing him, providing a retroactive explanation for the buffoonish behavior the character often exhibited in earlier appearances. Wally was one of the first heroes outside the group to learn the truth, which he was outraged by, especially since it shattered the idealized impression of Barry he remembered. Things soon got even worse for the third Flash.
In The Flash storyline “The Secret of Barry Allen” by Geoff Johns and Howard porter, which premiered alongside Identity Crisis in The Flash issues 214-216, Green Arrow gave Wally a letter Barry wrote him before he died in Crisis on Infinite Earths. In it, Barry tried to explain to his nephew why he made the choice he did. As shown in Identity Crisis, Barry’s was the tiebreaking vote that decided to alter Light’s mind, which was a particular shock to Wally. In the letter, Barry admitted that he knew this was a mistake, but at the time he had believed that his wife Iris was killed by the Reverse-Flash, leading him to become a more ruthless crime fighter. He explained that soon after the Light incident he stepped even further over the moral line when he made a drastic choice to neutralize The Top, one of his regular Rogues who was growing increasingly powerful and dangerous.