The Agency is the public face of a shadow committee, consisting of military leaders, intelligence experts, and government officials. It is currently under control by Amanda Waller. In order to capture the Pact, the organization would work with the vigilante Batman to capture the group.
It is unknown who founded the Agency or what its main operations were. Officials in the organization were if allowed to, over local law enforcement with impunity and take over operations from the highest ranking official. The Agency had a long history of unethical operations, including civil rights violations, domestic black sites, and decentralized accountability. By the time Amanda Waller became its director, these accusations were silenced and the Agency was one of the most powerful law enforcement agencies in the United States.
Prior to Waller becoming the director, an Agency cell called SANCTUS had developed a bioweapon codenamed Project LOTUS. Although thought to be shut down by Waller, the organization survived and continued to operate in secret. Waller also used the Agency's resources to carry out operations, such as the disappearance of two whistle-blowers and cover ups of the true identity of the Riddler, a criminal they had employed as a SANCTUS researcher.
After learning that Riddler had escaped from a revived SANCTUS, the Agency began hunting the criminal down, hoping to find and dismantle the organization. They also began looking into associates that the criminal had inducted into his own organization, the Pact, and set out to capture them. Despite constantly tracking him down to multiple areas of the world, the Agency never successfully captured Riddler, due to his knowledge of their methods. Eventually, they would track the Pact to Gotham City, where Riddler had been active before his employment in the Agency.
Waller and a group of agents arrived at the Virago casino, having heard reports that the Riddler had attacked. After they subdued the last of the Riddler's men, they helped the GCPD round up the suspects and clear up from the attack. They also placed the victim of the attack, Rumi Mori, into a security detail. During this, Batman became acquainted with Waller, agents Iman Avesta and Vernon Blake.
Whilst the agency search for the Riddler, Avesta, and Blake later visited Bruce Wayne in his office to interview him on a person of interest, "John Doe". About a week later, another agent, Mario Hernandez, was kidnapped by the Riddler, forced to participate in a death trap, which he failed, and died. Batman and Commissioner Gordon would discover his corpse whilst investigating the building he was held in.
That same day, Avesta, Blake and two other agents were able to locate the Riddler on his personal ship, the Lady of Dublin, but were captured and held within the Riddler's death traps. Desperate, Waller allowed her agents to brutally interrogate Eli Knable, the Riddler's second in command and kept her agents observing Mori. When Batman was able to retrieve information about the Riddler's location, he put it through to the GCPD and the Agency, with the agents and Waller heading to the ship.
Upon arrival, Batman was able to free Agent Avesta but was captured by the Riddler and forced to either sacrifice the others, including Blake's, to save her or go through with the Riddler's game, deafening her in the process. Regardless of the decision made, Batman eventually broke free and captured the criminal, but he was shot with a poisoned dart and died. Believing the GCPD to be ineffective or have tampered with her operations, Waller had the Agency take control and forced the GCPD to step down from the investigations.
Whilst investigating the Lady of Dublin and rounding up the remnants of Riddler's men, the Agency sent their agents to investigate a series of explosions throughout the city. Waller and either Avesta or Blake, would be in charge of an investigation of GothCorp, where staff and security had been frozen in ice by an unknown individual.
If Batman calls Waller for help after his battle with Bane, the agents will help him out of a pile of rubble he was trapped under and investigate the GCPD's arsenal for anything that they could connect to the Pact. Using cartridges they find there, the scientists are able to make a counter-agent to Venom, which is later given to the vigilante by Waller.
Agents, including Avesta, followed and monitored Bruce Wayne as he infiltrated the Pact, to make sure he followed by Waller's rules. Wayne, as Batman would later advice that they would stop this, as it could lead to the group members becoming suspicious of him. At some point, Waller decided to give up the Riddler's body to the Pact, hoping that it would get their attention.
Whilst escorting the Riddler's body out of the city, the Agency were attacked by the Pact, who sought to retrieve their fallen comrade's body for their operations. Using an EMP generator from Wayne Enterprises, they deactivated the agents' stun pistols. Despite this, they tried to fight back, leading to multiple deaths and either Bane or Harley Quinn being left behind. Despite Wayne asking her to act, Waller stood by as the Pact stole Riddler's body.
After Batman was able to uncover the location of a SANCTUS base, Waller sent the Agency to arrest the Pact and retrieve equipment for future use. During the operation, they were able to capture Mr. Freeze and Bane, whilst "John Doe" and Harley Quinn was able to escape. With Freeze being infected with the LOTUS virus, the Agency planned to keep him to analyze the effects of the virus. However, Batman/Wayne can tamper with these plans by reducing the temperature in his confinements to help him attempt to combat the virus.
During the cleanup, an Agency taskforce infiltrated the Pact's lair to steal samples of Riddler's blood. To ensure Quinn didn't get samples from his corpse, they drained the blood from the criminal's body. They also captured Selina Kyle/Catwoman, after either finding her in one of Riddler's traps at the lair or managing to capture her during the attack on SANCTUS (depending on whether Batman gave her up as the traitor). Afterward, these samples were moved to cold storage, so that the scientists would be able to synthesize a usable version of the LOTUS virus to blackmail the other members. However, these samples were later destroyed by Avesta to prevent Waller from going through with her plans.
When Harley Quinn held a desperate attempt to hold the Gotham Bridge hostage for the stolen samples, the Agency was involved in securing the area. They would attempt to negotiate with her but refused to go through with her demands. Depending on how much he trusts John Doe, Batman's actions will affect how the situation plays out.
If Batman is able to trust John, the vigilante's alter-ego, Bruce Wayne, and Doe arrive to help defuse the situation. The Agency is told to let the two through to negotiate with Quinn, though with John being forced to take over the responsibilities when Wayne only angers her further. Depending on whether Bruce is able to trust John and keep Waller at bay, the following will happen.
If Bruce is able to trust John and keep Waller at bay, Quinn is successfully capture, though the Agency quickly turns on John when he refuses to hand over the LOTUS virus. He then attacks their agents and detonates the bombs. As he leaves, he promises the Agency that he will target them and reveal the corruption within their ranks.
If Bruce is unable to trust John or keep Waller at bay, he turns on the billionaire and the Agency. As the agents make an attempt to capture and execute Harley Quinn, John detonates the bombs and attacks them.
If Batman was unable to trust John, the vigilante is forced to interfere and tries to capture Quinn. After he is able to restrain her, Waller and the Agency attempts to get closer, but are unable to take a shot, due to Quinn holding a dead man detonator. When John Doe arrives to save the criminal, he takes the switch and detonates the bombs, causing devastation across the bridge and to the Agency's forces.
Depending on whether John Doe has become a vigilante or a criminal, the following actions will be taken by the Agency.
If Doe has become the vigilante Joker, the Agency begin searching for him and Batman, due to the former's possession of LOTUS and their association. After reports of John's associates being present at Riddler's lair, the Agency find and interrogate them, hoping to get the fugitive's location. When Special Agent Harrison attempts to execute one of them, Batman, having slipped past those guarding the site, stops them. The agents then attack Batman, but attacked by Doe (now calling himself "the Joker").
Working together, Batman and Joker subdue the agents, leaving some seriously injured in the process. Unable to match them, Harrison calls in for the Agency to send in Bane, who has been given a new version of Venom and seeking to kill Joker for his believed involvement in Riddler's murder. Battling the criminal, Batman and Joker are able to defeat him. More reinforcements arrive, forcing the two vigilantes to flee.
When Waller confronts Batman on the roof of the GCPD, a number of agents are present during the later part of the battle between them, Joker and their supervillain division. Eventually surrounding the two vigilantes, the Joker releases two bombs, both of which threaten agent lives. Regardless of which one Batman stops, the other kills at least eight people and injures eleven more, though it is currently unknown how many were actual members of the Agency.
During the fight, Joker captures and flees with Waller. Though they attempt to retrieve their director, the Agency ultimately lose the criminal after a high speed pursuit through Gotham. With the organization is placed into disarray. Desperate, they are forced to make a deal with Harley Quinn, granting her the title and privileges of a special agent in return for her help. Using their assistance, Quinn attempts to murder Batman and the GCPD, though is quickly subdued by the vigilante. If Tiffany Fox has joined the Agency, she is also present during Batman's investigation to locate Joker's hideout.
The Agency later learn that he is using the disused ACE Chemicals plant and retrieve Waller, Joker and Batman after the latters' battle. They are also forced to stop their manhunt for Batman in gratitude for his actions and a truce the vigilante has organized with Waller. The vigilante can also negotiate for them to either release Catwoman, place Quinn and Bane on trial, or for them to leave the resigning Avesta alone, despite her actions.
If John Doe has become the Villain Joker, the Agency are sent to a list of demands from him and Quinn. These include for them to withdraw from Gotham, though Waller is to be shot out of a cannon at the stroke of midnight. Despite these outlandish orders, they work with Batman and the GCPD to locate the criminals' bombs and defuse them. After Gordon returns with the location of every one in Gotham, they are able to find and defuse all of them with the GCPD's help.
Possibly before or during the chaos, Joker and his men assault a convoy escorting Catwoman out of the city, taking her and the surviving agents hostage. Forced into the criminal's games, the agents are all killed in his demented games, either through Joker's tricks or not being able to solve the problems. After being informed of Joker's lair at the Bonus Brothers Carnival, the Agency are able to arrive in time and are possibly the ones who find Wayne, Kyle, Joker, Quinn and their men. Whilst the former is taken for medical care, the others are arrested.
If Wayne chooses to use Waller's influence to affect he allies, the Agency's resources can be used to affect either Catwoman, Gordon or Avesta.
After the Joker's capture, Waller would order every operative to leave Gotham, seeing that the organization had no reason to stay in the city. She and every operative carry out their orders and leave.
- Amanda Waller - Director
- Vernon Blake - Special Agent (determinant)
- Tiffany Fox - Special Agent (determinant)
- Roger Harrison - Special Agent (determinant)
- Maureen Chan
- Renee Gladwell
- Tyson Borley
- Todd Marshall
- Lynda Farrow
- Suresh Pradeep
- Michael Finn
- Ryan Garcia
- Natalie Fried
- Heather Greenbaum
- Vince Rector
- Bradley Willis
- Jevon Banks
- T.R. Langley
- Martin Woo
- Lara Kilroy
- Trent Vimes
- Michaela Prince
- Kyle Standish
- Vicki Rooney
- "Patrick" (determinant)
- SANCTUS - Researchers (partnership dissolved)
- "Riddler" - SANCTUS Researcher (deceased)
- Mario Hernandez - Special Agent (deceased)
- Iman Avesta - Special Agent
- Vernon Blake - Special Agent (determinant)
- Roger Harrison - Special Agent (determinant)
- "Patrick" (determinant)
- In the comics, the Agency is an independent branch of Task Force X, an international organization associated with the original Suicide Squad, albeit without ties to Batman or his rogues gallery. This version is loosely based on A.R.G.U.S., an organization in DC's post-Flashpoint timeline that is run by Amanda Waller.
- It is heavily implied that the person who recruits Floyd Lawton/Deadshot at the end of Batman: Sins of the Father is a member of the Agency, possibly Waller herself.