Amanda Waller is the current President of the United States of America. After Superman executed members of the Chaos Society to end their killing spree in the Metropolis Central Station, much debate about him followed. Waller conferred with her national security adviser Jack. With no good coming from allying with him or trying to destroy him, Waller pushed for something since most of the world thought Superman was a product of the U.S. government anyway. Jack advised her to watch Superman and study him for weaknesses then hope for a bigger crisis to come along and push him off the front page of newspapers. After Superman, Wonder Woman, and Batman defeated and killed Imperiex, they were approached by President Waller, Colonel Trevor, and Dr. Luthor. She insisted they needed to talk for the sake of the world. She introduced herself, then Trevor as the head of A.R.G.U.S., and Luthor as her friend and adviser. Waller then revealed the three aircraft above them had enough payload to level a city. Superman, Batman, and Wonder Woman complied and were taken to Cheyenne Mountain Complex.
President Waller asked the obvious question of what to do with them. After discussions became heated following Luthor's claims they were to blame for Imperiex and the Forever People, Waller interceded and asked them what they thought average people thought as they saw them fly above and act as judge, jury, and executioner. Superman had enough but Batman admitted he understood Waller's point. He contested they should be locked away at the bottom of the mountain. Superman insisted the people saw them as heroes. Waller played a news report by Lois Lane with protesters outside the White House. Superman deferred to Waller. She proposed a pact that involved the formation of a government task force later known as the Justice League.
During the Brainiac incident, Waller deferred to Dr. Sivana on how to neutralize the threat if tanks were ineffectual. She was aghast at the thought of sacrificing millions of lives to kill Brainiac with a nuclear warhead. Sivana insisted it was that or lose the entire eastern seaboard. One of Waller's aide reported he couldn't reach Superman. With no other plan, Waller called the Pentagon and ordered the nuclear strike. She got word Kobra was going to make an attempt on her life with a new weapon on the day of her inauguration. Steve Trevor was sent to neutralize the threat. Some time later, Waller sent the Justice League and Trevor to find the terrorist organization that stole her files. The murders of three scientists associated with Project Fair Play in a short time span convinced Waller to send in Trevor to investigate. After the forensic evidence was found to implicate the League in the murders, Waller has a secret conversation with them and recommended they volunteered on their own to speak to the authorities. She believed that would relieve some of the pressure she was feeling in the political community.
After NASA confirmed Dr. Luthor's ship in space was destroyed and Superman was his last visitor, President Waller knew she couldn't protect the League anymore. All the scientists associated with Fair Play were murdered. She sanctioned Project Fair Play and ordered Metropolis to be evacuated. Trevor was authorized to order the Justice League to surrender and use lethal force if they refused to comply.