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Nicknamed "the Wall", she is a former congressional aide and government agent often placed in charge of the Suicide Squad, a semi-secret government-run group of former supervillains working in return for amnesty. She also was the former leader (code rank: White Queen) of the covert-ops organization, Checkmate. She later served as Secretary of Metahuman Affairs under President Lex Luthor, before being arrested in the wake of Luthor's public fall from grace. Waller was recently reassigned to the leadership of Checkmate as White Queen, but has been forced to resign because of her involvement in Operation Salvation Run.
Amanda has been established as a widow who escaped Chicago's Cabrini-Green housing projects with her surviving family after one of her daughters and her husband were murdered, Waller eventually obtained a doctorate in Political science (as revealed in Checkmate v.2 # 1 where she is addressed as "Doctor Waller") and became a congressional aide. During that work, she discovered the existence of the first two incarnations of the Squad. Taking elements from both of these, she proposed the development of its third incarnation to the White House and was placed in charge upon its approval.
Federal service years
The Agency was formed by Amanda Waller to serve as a small, quasi-independent branch of Task Force X. Valentina Vostok brought former NYPD Lieutenant Harry Stein into the Agency as an operative. Amanda Waller later promoted Stein to the command position and demoted Vostok. Harry Stein would later re-organize the Agency and name it Checkmate.
Waller's tenure as the official in charge of the third Suicide Squad was tumultuous and controversial. Despite many successes, she developed a habit of defying her superiors in Washington in order to achieve goals both legitimate and personal on more than one occasion. The earliest conflict between her and her superiors revolved around the leadership of the Suicide Squad. Although she proposed that the Bronze Tiger, the man she had helped out of his brainwashing, lead the team he was instead relegated to second-in-command, and Rick Flag Jr. was made the leader. Waller feared the situation to be racially charged, related to not only her own status as a black woman, but also Bronze Tiger's own skin tone.
Her relationship with the Squad itself was one of mutual dislike. Most of the team's criminal members didn't really take to Waller's methods (most notably Captain Boomerang), and even the team's heroes were often at odds with Waller. Waller's inability to deal and compromise with her people led to the departure from the team of Nemesis, the death of a US senator and thereby indirectly to the death of Rick Flag Jr. Those type of conflicts, however, were not only limited to her superiors and her team, but also extended to Batman, who opposed the forming of the Suicide Squad (although he would later help to re-form it). Nonetheless, the team remained loyal to her, often choosing to side with her instead of the government.
It was ultimately revealed that the reason that Amanda Waller even kept the heroes such as Nightshade around, was in order for them to act as her conscience. Over the course of her first run with the Suicide Squad her actions became increasingly erratic as she fought to retain control of the Squad. This was heightened by the public reveal of the Suicide Squad, and her being officially replaced, although her 'replacement' was in fact an actor, and Waller remained the team's director.
Even that secret would eventually be revealed and Amanda Waller would be put on trial. During this time, the Squad also became involved in an inter-agency conflict in a crossover between the Checkmate and Suicide Squad titles called the Janus Directive.
The Squad's rebirth
Waller is eventually pardoned and released a year later to reorganize the Squad as a freelance mercenary group at the behest of Sarge Steel to deal with a crisis in Vlatava, Count Vertigo's home country. Afterwards the Suicide Squad performs a variety of missions.
During the course of her renewed tenure with this team, Amanda Waller became closer to her operatives, even accompanying them on their field missions. This allows for her and her team to bond more effectively, although she retains her dominant and threatening personality.
One of the field missions is against her will, as many members of the Squad, Waller included, are forcibly kidnapped and taken to Apokolips. This is because team member Duchess remembered her past as Lashina of the Female Furies and wished to return home with suitable sacrifices. The Squad takes fatallities battling Apokolips forces, with Waller personally confronting Granny Goodness.
Waller quits after after a latter field mission, in which she personally takes down the seemingly immortal dictator of a small, South American island nation.
Soon after, Amanda Waller organizes many superheros to confront the villain Eclipso. Again she would confront Sarge Steel. Her first attempt at a team, formed with the assistance of Bruce Gordon and his wife Mona, did not go well. Most of the team are brutally murdered infiltrating Eclipso's stronghold. Her second attempt with a much larger team has much more success.
She eventually rejoins federal service, initially as Southeastern regional director for the Department of Extranormal Operations. She is promoted to Secretary of Metahuman Affairs as a member of the Lex Luthor Presidential Administration.
Lex Luthor's brief tenure in office leads to Amanda Waller being jailed. This doesn't last long. She is released and Luthor's successor, Jonathan Vincent Horne, orders her to take command of the secret agent organization Checkmate. This orginzation had been shaken up OMAC Project debacle and the related murderous leadership of Maxwell Lord, whom Waller has had previous history with. Waller takes the rank of Black King until the United States and United Nations decide what to do with that organization. In the latter issues of 52, Waller is shown commissioning the imprisoned Atom Smasher to organize a new Suicide Squad to attack Black Adam and his allies. This ends with the death of Squad member Persuader and the expected public relations turn against the Black Marvel family.
In the revamped Checkmate series set in the One Year Later continuity, Waller is shown to have been assigned by the UN to serve as Checkmate's White Queen, a member of its senior policy-making executive. Due to her previous activities her appointment is contingent on her having no direct control over operations.*Checkmate vol. 2 #6* Regardless, she continues to pursue her own agenda, secretly using the Suicide Squad to perform missions in favour of American interests*Checkmate vol. 2 #7* and blackmailing Fire.*Checkmate vol. 2 #5* It is also implied that she may have betrayed a mission team in an attempt to protect her secrets*Checkmate vol. 2 #18* and facilitated an attack on Checkmate headquarters for her own gain.Checkmate vol. 2 #20
She is currently in charge of Operation Salvation Run, an initiative involving the mass deportation of supervillains to an alien world. When this was discovered by the rest of Checkmate she was forced into resigning as White Queen in exchange for their delay in revealing what the US government was doing. She continues to run the Suicide Squad, and has been implanted with nanotechnology to allow her to directly control Chemo during missions.
In other media
DC Animated Universe
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 by Superman and the Huntress who rescue him. 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 as well as 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 does not commit. Waller is one step away from being a supervillain, yet her motivations — and even, perhaps, her actions — are understandable to the viewer. She even 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. All of this makes Waller among the most morally complex and realistic characters featured on Justice League Unlimited.