Amanda Waller appears in the animated television show Justice League Unlimited, voiced by Emmy-nominated actress CCH Pounder.
This version of the character leads the top secret Project Cadmus, a group that was formed at the behest of the United States government to create a counterforce to the Justice League should they go rogue. To that end, the project creates the Ultimen. Perhaps the most profound relationship she has is one of mutual enmity and respect with Batman. She knows about his secret identity of Bruce Wayne which she revealed when she called Batman "rich boy" in the episode "Ultimatum," just as he was able to gather intel on her past. She however has chosen to keep his secret. This was also shown in the episode "The Doomsday Sanction" in which Amanda is clearly shaken after talking to Batman, and he has seen her point by the end of the episode. Most interaction between Cadmus and the Justice League is via these two individuals.
As detailed in "Ultimatum," the Ultimen is a team of artificial superhumans with implanted memories, created to be loyal to the government. In addition, the project includes a clone of Supergirl named Galatea (effectively a disguised version of Power Girl), revealed in "Fearful Symmetry."
When The Question discovers the project and is captured, Waller and Lex Luthor give orders to Dr. Moon to run a full interrogation on The Question which is interrupted when he is rescued by Superman and the Huntress. Lex Luthor takes advantage of the incident to momentarily hijack the League's satellite headquarters' binary fusion cannon to fire on the now abandoned Cadmus base with massive collateral damage to falsely implicate the League. While the government investigates the firing, Waller decides to take action. It is revealed that Cadmus created dozens of clone copies of the Ultimen team in order to attack the Watchtower; with Galatea leading them, they mount a full offensive against League HQ, intending to overload the reactor and destroy the Watchtower with the team on it. However, when Batman presents evidence of Luthor's deception, Waller calls off the attack and releases the senior Leaguers, who had turned themselves in as an act of good faith. With the Leaguers in tow, she personally goes to arrest Luthor and stops his attempt to transfer his consciousness into a potentially invincible copy of Amazo. It is revealed that Brainiac implanted a nano-holistic copy of himself within Luthor's body years earlier, during the Superman: The Animated Series episode "Ghost in the Machine", and the Justice League is forced to defeat the two of them combined. Unknown to them during this battle, Waller had ordered a massive airstrike on standby to kill the combined villains, the Leaguers, and even herself should the heroes had failed to stop the menace. All this occurred in the four-part arc in the second season, including the episodes "Question Authority", "Flashpoint", "Panic in the Sky", and "Divided We Fall".
The final episode of JLU's second season, "Epilogue", is set sixty-five years past the current Justice League timeline — years after even the events of the Batman Beyond series, as we see Bruce Wayne further deteriorated and Terry McGinnis an adult. Here, McGinnis discovers that he is a partial genetic copy of Bruce Wayne; knowing that the Cadmus Project was the only group to have technology advanced enough to alter DNA, he seeks out Waller to find out about his own origins. She reveals some of the future of the Justice League — at some point, the government will appoint a liaison with the League (a post Waller will fill for some time) and they will fight a reconstituted Royal Flush Gang, with Ace, from the Justice League episode "Wild Cards", leading them. Waller also reveals that she was responsible for changing Terry's father's genes; knowing that Batman would never have children of his own, she used Cadmus technology to create a child with his DNA, so the world would not be without a Batman.
"Epilogue" shows the complexity of the character; at the same time she is talking about the world needing a hero like Batman and about her faith in God, she also calmly explains that her plan to ensure Terry became a new Batman was to have Terry's parents murdered by Andrea Beaumont (also known as the Phantasm from the 1993 animated film Batman: Mask of the Phantasm) whilst he watched, murders Beaumont ultimately refused to commit, for it would dishonor all Bruce stood for. From that point on, Waller would never have Terry's parents killed. But when Warren was murdered by Derek Powers, the project was successful. Waller sees that Terry becoming Batman is a sign from God but tells him he can make his own life, not live the same as Bruce's. She advises him to make choices for the people he loves if he wants to or not. Waller admits that many of her actions have been reprehensible, and will have much to account for with God when her time comes, so she is not a self-deluding villain. It is also revealed that she had been keeping an eye on Terry his whole life.