- "You got that look in your eye. The kind that says you're trouble."
- ―Harley Quinn to Bruce Wayne[src]
Harley Quinn is a secondary antagonist in Batman: The Enemy Within. A masked criminal and a member of the Pact, her true identity was Dr. Harleen Quinzel, a former psychiatrist at Arkham Asylum and Blackgate Penitentiary. Whilst working with the group to retrieve a biological weapon, she became the one-sided crush of former patient "John Doe" and an associate of Bruce Wayne. Quinn would later betray the Pact and become one of the factors for John's transformation into the Joker.
From a young age, Harleen Quinzel was obsessed with psychological issues, due to her father's own struggles with his mental health. After graduating from Gotham State University as a Doctor of Psychiatry, she was placed in both Arkham Asylum and Blackgate Prison where she interviewed a number of inmates, including the mysterious "John Doe" and Oswald Cobblepot.
Over time, despite the help she offered to her father, he committed suicide some time after the riots at Arkham and Harley learned the mental illness he had was also hereditary. Whether it was a result of the trauma of losing her father and knowing she would suffer the same mental illness or the beginning stages of the illness itself, Harley suffered a mental breakdown and quit her job. Her eagerness to cure her hereditary illness made her an easy target for the Riddler, Gotham's original super-villain, who recently returned to the city to finish recruiting individuals to complete his criminal organization, The Pact.
When Riddler revealed that he was planning an attack on the organization SANCTUS to retrieve the experimental virus, Project LOTUS, Harley was easily drawn into his fold, knowing of LOTUS's regenerative capabilities, which she could use to cure her hereditary illness. However, Riddler, who truly lusted for revenge over SANCTUS and the Agency, did not inform Harley that LOTUS would only make her condition worse, knowing she would not agree to his plans if she had such information. Renaming herself as Harley Quinn, Harleen became a criminal and also recruited her former patient, John Doe, into the Pact as well, knowing of John's potential to incite violence and chaos from their previous therapy sessions, after he was legally discharged from Arkham Asylum.
Despite the group being founded and led by the Riddler, Harley and the others worried about his choice to draw Batman's attention, due to the possible risk of exposure.
During the Pact's joint attack on various places in Gotham, Harley attacked the City Brokerage without assistance from any of the Pact's men. She murdered an unspecified number of staff and security guards; mostly with her handgun but some were killed by mallet. She was able to leave the scene with $4 million dollars of stolen diamonds and the contents of a security deposit box.
The next morning, Quinn received a message from John that one of his "friends", billionaire Bruce Wayne, was looking to join the Pact and help them in their operations. Harley decided to meet with Wayne in person and arranged to meet the two outside the Stacked Deck bar in the East End. According to Bane, Harley was originally planning to murder Bruce following the initial meeting.
As John hotwired a car, Harley slipped in and held a gun against Bruce's head, asking him why she should spare him. Regardless of the reason given, she and Bruce conversed on the reasons why he was joining the Pact and what was expected. After sending John to get her a slushy, she and Bruce also talk about him and how he was still "finding himself". When John returned with the drink, they left for Wayne Enterprises, though Harley told him what Bruce had said about him. Upon their arrival, Harley told Bruce that he was to retrieve the Phalanx Key from his company, with the results of this exercise proving whether he was worthy of the Pact.
Though she and John were asked to remain outside, they followed him into the building and knocked a security guard unconscious. Harley also met Regina Zellerbach, during which she threated her, only to be called back by Bruce. After being taken down to the lab through Bruce's personal elevator, she looked through the contents of the lab whilst the billionaire unlocked the vault. During this, she noticed an EMP Generator and decided to also steal it to help make their job a little less messy.
- If Bruce is not able to convince Tiffany Fox to stay quiet or lied to her about her father's death, Harley will capture her as she tries to escape the lab. Noticing that she has the Phalanx Key, she tries to find out who she is and why she had tried to steal it. When Tiffany confronts her and John on their involvement in Lucius's death, Harley denies involvement and tells her that Bruce is planning to join the Pact to test his loyalty. Regardless of whether he chooses to agree or deny her comments, she lets Tiffany escape.
When John gave her the Phalanx Key, she thanked him for giving it to her and listened to his story. She also asked John to steal the EMP generator and the trio left the building. Some time later, she and John split with Bruce to talk to the other members into letting him into their base. After they agreed to let him in, Harley set some of the group's men to meet with Bruce and bring him to the lair.
When Bane showed concern over letting him into the group, Harley tried to defend her decision and convince him to give him a chance. She also untied Bruce so he could turn off the EMP Generator, after John "accidently" set it off. After he was able to, Harley asked Bruce to talk to her in her office. There, she apologized for her behavior at Wayne Enterprises and why she put on the "Harley Quinn" persona. Harley also gave him some advice on how to approach Bane and Freeze. If Bruce learnt about her father, he may also talk to her about it. Despite threatening him, Harley admits to being impressed by his investigation. After talking about approaching the other members, Bruce left to see if he could get their approval.
After watching him beat down a member of Bane's gang, Harley alerted the rest of the Pact that their target was on the move. After holding a vote to see whether Bruce was to join the Pact, they launched their assault the Agency convoy transporting the Riddler's corpse. Harley, along with Bane, assaulted the agents and tried to keep them away from the escape vehicle. Depending on who Bruce chooses to help, the following will happen.
- If Bruce chooses to head off Harley Quinn, the two will work together to battle the agents, though Bruce will subdue the target non-lethally and save him from certain death. Though Harley admits having fun, she is disappointed for Bruce stepping in to stop her from killing the agent. As they escape, Harley tries to tell Bane to leave the agents but leaves him when he doesn't respond.
- Upon returning to the Five Points, Harley complements Bruce for his actions during the fight and argues with Freeze about leaving Bane behind. She also lets the billionaire open the case containing Riddler's corpse and reveals why they needed to retrieve it. Harley is present when Catwoman returns with a component required for the next part of their operations.
- If Bruce chooses to head off Bane, Harley will continue to engage the Agency. As the Pact leaves, she curses out loud, but continues to engage the Agency. John, having fallen for Harley, tries to convince the others to go back for her, but they refuse to, believing her to have either captured or killed.
Depending on whether Bruce chose to leave her or Bane behind, the following will happen to Harley.
- If Bane was left behind, she interacts with Catwoman and gives her the task of using the device collected, a retinal scanner, to copy Riddler's eyes. Not wishing to touch the corpse and wanting to get on with business, she gives Bruce the task of helping her and collects the diamonds she stole from the safe. When she and the other members return, she gives Catwoman half the agreed amount, promising the rest when they break into the SANCTUS black site. Moments later, Bane returns with the remainder of his men.
- If Harley was left behind, she is able to escape the Agency and the GCPD, though kills a number of officers and agents. After managing to escape them, she returns to the Old Five Points, having begun to suspect a mole.
After Bane ordered his men to execute her, Harley defeated them single-handed. Revealing her suspicions that there was a mole in the group, she took control of the group and began making accusations against Bruce, only to be brought back when one of their men objected. Shortly afterwards, she asked Bruce to talk to her and revealed one of Riddler's laptops, which she had acquired after his death and was encrypted. Despite knowing most of the plan to take down SANCTUS, Harley revealed that he had kept the location of a black site secret. She asked him to investigate the criminal's hideout and find out the information. She also suggested bringing John along to help him, though also allowed him to bring Catwoman as well.
When Bruce returned from the operation, Harley found him observing Bane's interrogation of the man who had stood up for him. After witnessing the criminal be killed by an overly aggressive punch, she decided to take over the mole hunt from Bane, deeming him too incompetent to do so. After noticing Bruce and John interacting with each other, Harley butted in to find out what they had found at the black site. When Bane challenged her on the loyalty of the two, she retorted about John's supposed loyalty. However, when John offered to help her find the mole, she dismissed him and asked to talk to Bruce.
Having suspected he had given John advice on becoming independent, she asked to talk to him. Revealing a makeup kit, she told him how it was one of her "favorite toys" and asked him about what else he believed was another one of her favorites. After Bruce guessed, she told him how she enjoyed her control over John and told not to interfere with him, threatening to kill him.
Harley later discovered that the laptop had gone missing and began interrogating the other members and employees of the group. Eventually, she deduced two suspects: Bruce or Catwoman. If Bruce had been able to keep Tiffany hidden or not told her about Project LOTUS, John will tell her himself. After revealing to John that she had narrowed Bruce down as one of the possible traitors, she decided to follow his request to let him interrogate the billionaire and gave him to advice when it came to interrogation.
When Bane returned with Bruce, having found him outside of the Bodhi Spa, she covered for him being there and sent him to get his men ready to raid the black site, also telling him to get Freeze to prepare a cryogenic chamber. She then invited Bruce into her office, where she began interrogating him. Asking about his views on killing others to prove a point, she then questioned his true intentions for joining the Pact and revealed her "soft spot" for him, due to the similarities between him and her father.
After applying makeup, she revealed that the laptop had gone missing and she had narrowed it down to him and Catwoman. Believing him to care about Tiffany, she threatened to harm her if he turned out to be the traitor, leaving him to be interrogated by John and listened into the interrogation. When she returned, John claimed that he had found out who the traitor was, leading her to personally ask him. Depending on what Bruce chooses to do, the following possibilities will happen.
- If Bruce chooses to blame Catwoman as the traitor, she orders her men to bring the thief up for execution. After thanking John for finding this information, she promises him that they will do many "bad things" together. She, Bruce and John later arrive as their men prepare to execute Catwoman in one of Freeze's cryogenic chambers. After Catwoman damages the planned execution method in an escape attempt, she orders their men to place her into one of Riddler's murder boxes and leaves with the rest of the Pact to raid the blacksite.
- If Bruce takes the blame for being the traitor, she orders her men to bring him to the execution chamber. After thanking John for finding this information, she promises him that they will do many "bad things" together. They then escort Bruce to Freeze's cryogenic chamber and order their men to free Catwoman. Despite John's pleas to spare Bruce, she ignores his request and tells Freeze to activate it. Whilst the other's leave to raid the blacksite, she promises Bruce to carry out her end in killing Tiffany, leaving him to die in the chamber.
Depending on who Bruce blamed as the traitor, the following will happen to Harley.
- Upon arriving, Harley and Bruce are the first to enter and deal with the receptionist at the Spa's counter. After finding the hidden entrance, she bypasses the retinal scanner with Catwoman's goggles and coordinates the Pact to deal with defenses. When Bruce is separated and tries to carry on without the others, she realizes he has betrayed them and orders the others to kill him.
- After they break into the lab, Harley stands by as Bane tries to kill Bruce and attempts to extract the virus with Freeze. When he does, she decides to betray the other members and leave them behind for the Agency. As Freeze is stopped by Bruce, she knocks the vials out of his hands and escapes with the remaining one. She then locks him in the airlock and bids the others goodbye whilst the Agency arrives.
- Alongside the other members, Quinn urges them to perform as much violence and carnage as possible, killing multiple members of SANCTUS and the Bodhi Spa. After making it into the lab, she leaves Catwoman to stand guard whilst they extract the virus. As Freeze does so, they are confronted by Batman, who followed them into the lab.
- Engaging the vigilante, Quinn is either easily knocked aside or pulled into battle with Catwoman, who switched sides to stop them. If the latter occurs, she is able to gain the upper hand and defeat the thief. Regardless of whom she fights, Harley is unable to prevent Batman from destroying Project LOTUS's incubators with either Bane or a Sticky Bomb. As Freeze attempts to escape with the samples, she knocks the vials out of his hands and steals the remaining one. She then locks him in the airlock and bids goodbye to Batman and the others, escaping as the Agency arrives on the scene.
Following her escape, Harley tried to return to the Old Five Points and steal samples of Riddler's blood. When Harley returned to the base, she found that the Agency had found their lair and stolen samples of Riddler's blood, along with draining his body to ensure she couldn't take anymore. Meeting John there, who gave an eyewitness account of what had happened, Harley lost her temper and hit him. She then left to make another plan to retrieve Riddler's blood from the Agency.
Returning to a lair she and John had set up, she planned to hold the Gotham Bridge hostage. After creating a set of homemade bombs, she loaded them into the last of the GCPD armored vehicles and rigged them to a dead-man switch. Arriving around midnight, she made her presence known to the Agency and waited for them to turn up. Depending on Bruce's interactions with John, the following will happen.
- If Bruce had chosen to believe John, he arrives with him to try to help to get Harley to surrender. Having made her demands, Harley takes a number of hostages and makes her demands to Waller. When John and Bruce arrive, she is surprised to see the two appear and, despite Waller's insistence that Riddler's blood has been destroyed, talks with Bruce. Despite the billionaire's attempts to talk her out of it, Harley refuses to negotiate with him. If Bruce decides to let John negotiate with her, he seems to be able to get her to hand over the detonator. However, the actions he takes lead to Waller getting suspicious and sending her agents to incapacitate the two of them. Depending on whether Bruce is able to trust John, the following will happen.
- If Bruce is able to trust him, John is able to get her to hand over and incapacitate her. After being handed over, Harley is taken into Agency custody. It is unknown whether they were able to get her off the bridge before John set off the explosives.
- However, if Bruce is not able to trust John to negotiate or gets suspicious when he tries to get her to surrender, she hands him the detonator as the Agency gets closer. With John's faith in Bruce finally shattered, she wins over his loyalty. However, whilst they are distracted by his speech, Waller's agents slip behind and capture her. As they prepare to execute Harley, John sets off the explosives and the two flee to the railing. Impressed with John's actions, Harley kisses him and leaps off the bridge, the two disappearing into the night.
- If Bruce is unable to believe John, Harley is confronted by Batman as she sets up the explosives. After realizing the vigilante is there, she tries to attack him, only to be incapacitated. Despite the vigilante's insistence to stand down, Harley reveals the detonator and activates it, making her demands to Waller and the Agency. Despite their claims that Riddler's blood has been destroyed, Harley refuses to give up, leading to Batman to try to get either the detonator or the vial of LOTUS she is holding away from her with his grappling gun.
- However, just as he does so, John arrives in another vehicle and crashes into her van, releasing the bombs onto the bridge and causing Batman to miss. Although surprised at his appearance, she listens to him as he proclaims his loyalty for her and, seemingly smitten by his words, hands over the detonator. She stands by as he detonates the bombs and causes damage to the bridge and flees to the railing with him. After watching John rant to Batman on how he has made him, she admits being impressed by his actions and kisses him, cementing his fall into villainy. The two then leap off the side, escaping into the night.
Depending on whether Bruce/Batman believed and/or trusted John, the following possibilities will happen to Harley.
- If Bruce trusted John, Harley is put into Agency custody and made part of the organization's special taskforce. Along with being placed in a collar to ensure her cooperation, the Agency also give her a new mallet with an electroshock feature. When Batman and John, now calling himself "Joker", are made targets of the Agency, they deploy Quinn and the other members to help capture them.
- Harley, along with Bane and Catwoman, are present when Waller confronts Batman on the roof the GCPD headquarters. She showed amusement when Batman reveals blackmail on Amanda Waller, laughing at the turn of tables. During the confrontation, Batman can try to negotiate that she and Bane are handed over the authorities to stand trial, which Waller agrees to if he hands over Joker. Regardless of how the conversation plays out, after Joker makes his presence known, Harley tries to bait him out. At Waller's orders, she attacks him but Batman engages her in battle. Though she is helped by her mallet, Quinn is temporarily subdued when the vigilante uses her hammer's shock feature against her. When the Agency finally corner Batman and Joker, Harley, along with her comrades, is in the path of one of Joker's bombs. Regardless of whether Batman chooses to save them or Waller's agents, Quinn survives unharmed.
- After Waller's kidnapping at Joker's hands, the Agency, desperate to find their director, temporarily give Quinn the status of Special Agent. Given all the responsibilities as other agents, she appears on the scene of Joker's first attack, where she discovers Batman and former Commissioner James Gordon investigating the scene, though Tiffany Fox, now either an agent or one of Batman's allies, may also be present. After hearing them discover Joker's location, she orders an Agency helicopter to open fire and attacks the group, but is eventually subdued by Batman, whilst the copter is called off by the GCPD. As she is arrested by officers, Quinn claims that the Agency will free her from prison, though Gordon assures her that she will not escape this time.
- Harley's fate is determined on the deal Batman made with Waller. If he chose to lock up her and Bane, she stays in custody and is sent to Blackgate prison. However, if he chose to free Catwoman or keep Avesta unharmed, she will be released and taken out of Gotham by the Agency, to be kept as an asset of the division.
- If John chose to rescue Harley, the duo set up base in the abandoned Ace Chemical Processing Plant, using its facilities to manufacture the LOTUS virus. The two also recruit more individuals into their gang and set up plans to get revenge against both Bruce Wayne and Batman. Whilst they plan to set off dispensers of the virus around Gotham to torture Batman, Harley plans to use survivors' blood samples to create the cure, either not knowing or ignoring warnings given by Batman. As revenge against Bruce, Harley and John, now calling himself "the Joker", also decide to let the first one off at Wayne Enterprises.
- After being informed about Bruce's arrival at Wayne Enterprises, Harley and her men attack the board room, taking Bruce and the entirety of the board hostage. Whilst Bruce tries to negotiate their freedom, Harley refuses, signaling Joker to make his presence known. After Joker reveals his relationship to Bruce, Harley brings a LOTUS dispenser and orders her men to put gas masks on. After releasing, she uses her hammer to kill Regina Zellerbach and makes a video threatening Gotham. After checking for survivors, Harley knocks out Bruce and releases the virus through the company.
- Harley later appears as part of the "family meal" she and the Joker have organized. After Bruce arrives with Selina Kyle and Tiffany Fox, she welcomes the group and reveals she has the controls for Selina's collar, forcing the group into cooperating. During the meal, she tries to force Bruce to eat a piece of meat with an object hidden inside it and makes out with Joker, in an attempt to make their "guests" feel awkward. After her men bring in the virus dispenser, Harley prepares to activate it, only to be talked into playing a game of "Never Have I Ever" with Bruce and his friends. During it, she admits to all the actions, including lying, manipulation and murder, though is let off and attacks Selina for each of her admissions. During the game, she is briefly distracted by Tiffany, who insults her.
- Eventually, Harley tires of the game and decides to release the virus. Just before she is able to, Bruce either reveals Joker's obsession with him or that he has given the GCPD the locations of the LOTUS dispensers behind her back. Angered at this betrayal, Harley tries to kill her partner and release the LOTUS virus, though Bruce disarms it with a knife he retrieved during Tiffany's distraction before she can detonate it. After he frees his allies, Harley and Joker engage Bruce in combat, though she incapacitates Selina with her shock collar. Eventually, after Bruce deactivates the collar, they are forced to fight the two, though Harley is quickly defeated by Bruce. When Joker leaves her behind to escape, Harley, angered at his betrayal, tries to chase after him, but is quickly stopped by Selina. Whilst Bruce goes him, Quinn is easily defeated by their former ally.
- Harley Quinn is later captured by either the Agency or GCPD. She is eventually handed over to stand trial for her actions, eventually landing a sentence in Blackgate Penitentiary.
Though initially a calm and collected young doctor, Harley's breakdown caused her to look for excitement wherever possible. She seemed to have an enjoyment for chaos and trouble, choosing to start fights or threaten others at seemingly random times. Harley seemed to be unstable, but it remains unknown whether this was put on to throw off the other members of the Pact, making sure she was never taken advantage of, or part of the aftereffects of the breakdown. Harley also seemed to suffer from violent outbursts whenever something didn't go her way, which made her all the more dangerous when stirring up chaos around her.
- Sledgehammer/Mallet: Harley would often carry a large sledgehammer with her at all times, often to destroy objects or cause trouble. Though a very deadly weapon, Harley was able to hit it with enough force to knock someone unconscious and not kill anyone. This was often her preferred weapon in close-quarters combat and whilst on riots with the Pact. If Harley is captured by the Agency, she is later given a new mallet with an electroshock feature, allowing her to stun her opponents.
- Pistol: Harley would use a customized pistol whist out in action, though it is unclear how often she used it. The pistol seemed to be used whenever she wished to kill someone and in battles where close quarters was not a viable option.
- Mannequin Bombs: During the confrontation at the Gotham Bridge, Harley used mannequin heads stuffed with C4 explosives. The bombs were quite destructive, being able to cause structural damage to the location when detonated. Quinn also rigged them to a dead-man switch, which would detonate them if she released the switch under any circumstance. The bombs would later inspire "John" to create more when he became the Joker.
- "Don't turn around. All right, Wayne. Ya got my attention. Gimme a reason why I don't redecorate the windshield with your noodle."
- "Stay out of this, Puddin'. Grown ups are talking."
- "You're on, Brucie-boy."
- "That was beautiful Mr. J. I always knew you'd do great things."
- "You backstabbing piece of crap"
- "Uh-huh, sure. You gonna tell me ya love me, Wayne? I like a little romance when I'm gettin' screwed."
- This version of Harleen Quinzel was not driven to crime or insanity through the Joker's manipulations. Instead, her influence, if not broken, leads "John Doe" to becoming a villainous version of the Joker.
- Whilst Harley's design is based on that present during The New 52, she uses a sledgehammer, much like her pre-Flashpoint counterpart used a mallet.
- A baseball bat can be seen in her office, a callback to her preferred weapon within both the Arkhamverse and the comics (post-Flashpoint).
- It's possible for Harley to not encounter Bruce as Batman at any time during The Enemy Within, depending on the decisions made by the player.
- Harley serves as the main antagonist of "The Pact", "Fractured Mask" and "What Ails You". She also serves as either a minor or secondary antagonist in "Same Stitch" depending on the version of Joker created; the former available through the "Vigilante Joker" and the latter through the "Villain Joker".