Five years before the main events of the comic series, Harley discovered she was pregnant with the Joker's child. Not wanting the baby to be brought up in their lifestyle, Harley left the Joker for almost a year to have the child, a girl she named Lucy, who she left with her sister. When she returned, she was saddened to discover the Joker had never noticed she was gone.
Quinn is first seen in disguise on the docks with Lois Lane and Jimmy Olsen watching her, unaware it is a trap until the Joker murders Jimmy with a gunshot to the head. Harley sheds her disguise alongside the Joker as they kidnap Lois. Harley is not seen again until the Justice League learns that she and the Joker have hijacked a nuclear submarine. When Superman enters the sub, he sees Harley and the Joker in scrubs looming over an unconscious Lois.
When the Joker gasses Superman with kryptonite laced fear toxin stolen from the Scarecrow, Harley joins the Clown Prince of Crime in mocking a reeling Superman. Superman flies off to battle a suddenly appeared Doomsday, murmuring about Superman. Afterward, Joker informs Harley it is time to leave. Though Harley is rather reluctant to leave the sub after she has named it 'Gunther'. Joker reminds her that the heroes "will hit us over and over again," and she relents.
After that she cheerfully bids "Gunther" goodbye, but it is too late and the two are subdued by a projected hand from Green Lantern's ring. Harley remains silent as Batman and the rest of the League realize exactly what she and the Joker have done, save for a single comment about the submarine's name, and gleefully hugs the Joker as Metropolis is destroyed and millions die in an instant.
Harley is in a police car when she learns of the Joker's death at Superman's hand. She dejectedly murders the two officers in the car and escapes in the vehicle to one of her and the Joker's hideouts, mourning the death of her puddin', and seeing no more joy in the world. After crashing the vehicle, she enters the hideout, a closed novelty joke toy maker and suits up in her costume. Green Arrow suddenly arrives, an arrow notched in his bow, but Quinn injures him with a grenade. Harley approaches Arrow with a massive mallet, apologizing for how it has to end and compliments his beard.
She strikes him with the mallet but it turns out to be a squeaky hammer. She pulls out a gun but her shot is deflected by Green Arrow shooting an arrow into the gun's barrel, which Harley finds amazing. Arrow quickly captures her with a trick net arrow, to which Harley responds, "You suck."
Green Arrow drags Harley into his Arrowmobile and when Harley asks him if he's taking her to Superman, Arrow denies this and explains he's taking her somewhere safe from Superman, though he makes it clear that he's only doing this so Superman won't make another mistake by murdering her. Harley annoys Arrow throughout the ride, prompting him to trick her into unconsciousness by giving her a trick arrow that releases knock-out gas in her face. Once more, Harley manages to slur before passing out a "You suck."
When Quinn comes to, Arrow reveals he's brought her to his Arrowcave, chained her to a pole and assures her that Superman will not be able to find her due to the lead lining the walls of the cave. Harley reminisces about the Joker who used to knock her out and handcuff her "Every Thursday," and goes on to mock the name of Green Arrow's hideout, suggesting he call it 'The Quiver' instead. Green Arrow begrudgingly admits that it's a better name.
Arrow tells her he has to leave and advises her not to try an escape with a 'fake hand'. Harley reveals she has a fake mustache instead of a fake hand, tearfully revealing the hand was the Joker's gag. Harley then ask Arrow, "Have you ever loved someone you knew was wrong for you? Someone who would hurt you over and over again and hurt those around you but you could forgive them because losing them would hurt even more?"
Arrow is shocked by her words, stunned he is able to relate to them. Harley goes on to admit that she knew the Joker was a "Bad Guy," with Arrow interjecting he was a "Genocidal Psychopath," but he was Harley's. Before Arrow leaves, Quinn asks from him for a "Little maniacal laughter?" At first Arrow refuses, but after seeing Harley put on her fake mustache he bursts into a fit, and Quinn thanks him.
Some time much later, Harley Quinn is being escorted in handcuffs by Green Arrow to Arkham Asylum. Harley is hesitant in Arrow bringing her here, arguing that the fire she started in the Arrow Cave was only a 'little' one. Arrow counters that it was actually an uncontrollable blaze. Harley further mocks his hideout's name and calls him a 'really crappy Robin Hood' by suggesting he robs from the rich to pay for himself.
Once inside the Asylum, Arrow assures her she will be safe there. When the orderly Kenneth spots Arrow and reveals the Justice League and Batman's presence, he quickly races off to prevent the inevitable confrontation between them, leaving Harley with Kenneth. Upon seeing the Man of Steel, Harley whispers his name before greeting Kenneth pleasantly. When Kenneth asks about her fake mustache, she reveals it is actually a lockpick while asking him "How many times have I broken your nose?" When he responds "Three times" she apologizes before knocking him out with an unseen punch to his nose.
Harley quickly heads to the security controls and monitors, looking for a certain inmate. When she finds him, she promises to free him, asking in return that he "Destroy the joint." As Green Arrow prevents a brawl between Batman and Cyborg, Harley announces her presence over the speakers before freeing all the inmates, saying, "Superman took away Mistah J. and now it looks like he wants to take us all away." She says she's giving them a chance to defend themselves along with some backup, in the form of the monstrous Solomon Grundy.
Harley cheers the inmates on as they attack the heroes, but tells them over the intercom, "Don't touch the green guy with the cute beard. I have a little crush on him, it's probably Stockholm syndrome but I'll take what I can get." Though not seen or heard for the remainder of the chapter, she, like many other superheroes and the inmates, are openly shocked by Nightwing's sudden death, Harley herself crying at the sight of his body being carried out by Batman.
Harley watches Superman's press conference in Paris from a TV, angrily glaring at the Man of Steel.
Harley is in one of her's and the Joker's old sewer hideouts in Gotham when Lobo comes bursting in on his motor bike. Shocked, she realizes he's not Superman and when Lobo tells her his name, she pretends to have never heard of him to distract him long enough so she can grab her hammer and smash it upside Lobo's head...which doesn't affect him in the slightest.
Lobo easily captures Harley and handcuffs her before putting her on his bike and flying off. When Lobo notices her putting on her fake mustache, he shares her sentiments on not having to justify a fake mustache. When Harley notices a strange pill, Lobo explains that if someone ingests it they gain invulnerability and super-human strength. As he's explaining this, Harley takes the lockpick from her fake stache and frees her hands, snatching the pill while Lobo continues to talk and swallows it. She then jumps off his bike and lands through a building.
To her amazement, she is completely unharmed and then jumps through a wall into another building, only to get sucker-punched by an annoyed Lobo. Harley then explains to Lobo that she's had time to think after coming to terms with the Joker's death, and she understands she was in an abusive relationship and angrily declares, "No one gets to lay a hand on me ever again." before punching him through a wall and into an oncoming truck.
She then steals his hog and flies off to Green Arrow's Arrow Cave, though due to not knowing where the brakes are, she crashes the bike inside the cave after bursting in, shocking Green Arrow and Black Canary. When Arrow asks what she is doing there, Harley says she needs their help but Arrow asks how she knew where the cave was and reveals she wasn't as bound as he thought she was, before again teasing him about the name much to Black Canary's amusement.
Both then realize who she stole the bike from and Lobo comes roaring in. Arrow and Canary manage to distract him long enough for Harley to rip his head off. Upon seeing their horrified reactions, Harley says, "I know what you're thinking." She then triumphantly holds Lobo's head up and declares, "Best. Team-up. Ever!"
With Lobo down for the moment, they secure him to a table and while he is unconscious, Harley hears him mumbling in his sleep, seemingly at war with himself. When he awakens, demanding to know what is going on, Harley, dressed in a doctor's coat, tells him, "This, Mister Lobo, is therapy."
When Harley tells him, "It's time to talk about your feelings." Lobo is horrified, with Harley asking if he's afraid of talking about them, with Lobo insisting he is not. Harley then tells Lobo she heard him talking in his sleep and tells him she thinks someone recently took his power from him and he is struggling with himself to get it back. When she reveals she knows he is the best bounty hunter in the galaxy, revealing she knew he who he was all along and only pretended not to know to throw him off.
She then asks what happened and if Superman somehow emasculated him, with Lobo insisting he wasn't, but when she asks him, "Then tell me why the best bounty hunter in the galaxy would waste his time hunting me?" Lobo then realizes hunting Harley is beneath him ("No offense taken.") and asks her what he should do.
Harley suggests he find a way to take back his power and a jubilant Lobo easily escapes his bonds, tells Harley they're done, and flies off on his hog.
A stunned Arrow and Canary approach her then, amazed she sent Lobo off, though Harley insists "No we beat Lobo. The team of Canary, Quinn and Queen." Arrow is happy for a moment before realizing she knows his real name.
Harley is revealed to have been hiding out in the Arrow Cave for some time since Green Arrow's death. Black Canary discovers Harley in the cave, with Harley holding a bow and arrow while wearing fuzzy slippers. When Canary demands to know what she is doing there, Harley replies, "Um...practicing archery in comfortable slippers?"
Un-amused, Canary reiterates her question and Harley admits she had no where else to go. Black Canary then orders her to leave and Harley refuses, throwing the bow and arrow aside. When Black Canary asks if she really wants to do this, Harley growls, "Bring it." before throwing her slippers with a cry of, "Fluffy slipper attack!"
When Canary catches them, Harley smirks and says, "You look calm for someone who's just caught exploding slippers." Canary quickly throws them aside but quickly discovers they're not explosives. "Of course not. That would be crazy." Harley says with a smile. Black Canary knocks Harley back with a sudden Canary Cry and Harley retaliates by grabbing her mallet and jumps to deliver a blow to Canary's head when she suddenly tells her to wait.
Harley stops mid-attack, confused. She notices Canary seems ill and she suddenly demands a nearby bucket. Confused, Harley gives the bucket to Canary, and is disgusted when she promptly vomits into it. Harley asks what's wrong with her and her eyes widen in sudden realization as she asks, "Is it morning sickness?"
Black Canary refuses to discuss this with her but Harley excitedly exclaims, "It is! You're preggers!" Black Canary can only throw up again, causing Harley to laugh. When Black Canary asks if she thinks it's funny, Harley admits she thinks it it's hilarious and when Dinah glares at her, she says, "Oh, come on. How is it not funny? You're a superhero with morning sickness. You save the world. And then throw up."
Harley then imagines Black Canary in her third trimester, but still wearing her fishnets and finds the image hilarious. Though Dinah wants to go back to fighting, Harley refuses and sits down next to her, saying she remembers how hard it was to be pregnant. Black Canary is shocked and asks if she had a child.
Harley is silent for a moment before saying they should go back to hitting each other, but Dinah presses the issue, calling her by her full name. Giving up, Harley admits she has a four year old daughter named Lucy, telling Dinah, "She likes tutus and toy cars. She especially likes putting tutus on toy cars. She likes the idea of a ballerina car." With a smile, she says, "I think that makes perfect sense."
Harley also admits that the Joker never knew he had a child, saying his work was too important. She then brokenly admits that he acted like he never knew she had left for almost an entire year. Harley admits her daughter is better off this way, having a normal life "filled with normal days and dancing cars." She then asks if the baby is Oliver's and admits she saw the news of his death.
She asks if Superman killed him and when Canary confirms this, she asks what she is going to do. When Dinah says she's going to make sure Superman can't hurt anyone else ever again, Harley says she wants to help her and while Dinah says she doesn't, Harley reminds her that Superman killed her man too, and she says she can do things Dinah can't, "Like fight without needing a bucket nearby." Turning serious, Harley says, "Please. Let me help." She is then accepted into the Insurgency.
Harley is seen alongside the rest of the Birds of Prey in their headquarters, looking at the groups slides of pictures from happier days in their pasts, Harley herself sitting next to Black Canary. A delighted Harley demands, "The next one, the next one!"
Harley is next seen when Commissioner Gordon brings Clayface to the resistance's headquarters, shocked to see the shapeshifter. When Gordon demands she come with him, Harley responds, "Oh, goodie, secret conspiracies--" and she is next seen with a nurses outfit over her regular costume as she draws a sample of blood from Clayface to test. After Renee Montoya leads Clayface away, Harley whispers in a suspicious Gordon's ear, "More than one way to get closure, Mistah G."
After Clayface is revealed to be a mole for Superman, Harley is next seen giving Black Canary bandages, and when Dinah protests, Harley shushes her and says, "They've got Hello Kitty on them. They're fashionable." When Montoya asks what they should do with Clayface, it is Harley who comes up with a solution. Later, Harley has secured Karlo by dividing his mass up and locking individual pieces into several glass jars that they cannot escape. A victorious Harley declares, "See? Closure!"
Seven months later, Harley has joined the Insurgency against Superman. Dressed rather scantly in civilian disguise, Harley visits Black Canary in the hospital after she gave birth to her son, Connor, claiming to be Dinah's sister to get visitor's rights. Harley is delighted to see the newborn child and comes with several presents, including a bow and arrow set ("Never too young for that."), a fake mustache ("That obviously needs no explanation.") and a muzzle.
When Dinah asks why he would need a muzzle, Harley explains that it was useful when she first got her hyenas. Dinah says Connor is a baby, not a pack hunter and Harley slyly reminds her of her Canary Cry ability and suggests Connor may inherit early. Grinning triumphantly, Harley hands the muzzle over to Dinah when she demands it. Harley then notices that Dinah's bag is glowing and asks, "Is that a thing it does?" When the bag suddenly produces a voice, Harley asks, "You can hear that too, right?"
Harley is silent as Dinah discusses with Guy Gardner the upcoming battle between the Green Lantern Corps, Sinestro Corps and Superman's forces.
As Batman makes a speech to the resistance over the upcoming battle against Superman's forces, while imploring everyone to say their goodbyes and to prepare themselves, Harley tearfully says, "No. Don't be like that. You need to stay behind. I couldn't handle it if anything were to happen to you..." to her fake mustache.
While almost the entire resistance reacts in a combination of stun and awe at the sight of the Green Lantern planet Mogo turning the sky green, Harley simply smiles as she watches while saying, "Naaaw. Pretty."
Harley is present alongside the rest of the resistance lead by Commissioner Gordon, and she is seen wearing a familiar purple hat and coat. When they receive word to attack the Hall of Justice from Oracle, Gordon warns Harley not to deviate from the plan. Harley doesn't respond, only smiles as she takes her super-pill.
Harley then goes up to the Regime soldiers stationed at the Hall's entrance and introduces herself by saying, "Hi! I'm the first wave." Before the soldiers have a chance to react, Harley opens her coat to reveal a large amount of explosives strapped to her chest. The bombs go off, allowing the resistance the chance they need to seize the Hall.
Harley survives the explosion thanks to the invulnerability provided by the pill, though her outfit is destroyed. After the resistance successfully defeat all the soldiers and subdue both Flash and Robin, Harley finds her old costume on display and puts it on, though she comments on the fact it was being displayed as, "Icky." When she sees that Lex Luthor has been captured, she asks, "Ooh. Once he's stopped struggling, can I please rub his shiny head?"
When Harley sees Catwoman contacting Oracle, she ecstatically exclaims, "Tell her I exploded!" before observing the unconscious Robin.
Harley is seen in an unknown location with the Flash bound and gagged onto a table. She is reassuring the Flash that he is just incapacitated and that the effects are not permanent. Harley then proceeds to play with his lightning bolt ear pieces, wondering aloud if he has those because he hears at super-speed before mockingly speaking very slowly into his ear.
Harley tells the Flash that she has been informed he's a nice guy who's made a lot of bad decisions and she believes he's been a bit brainwashed and that she's been there. Leaning on the Flash's chest, Harley tells him, "You get this guy who's all strong and powerful and confidant, and you just stare into his dreamy face and do what he says, right?" Harley reiterates that she understands and that she's going to get him through this before revealing she's been asked to reprogram him.
Harley assures him, "I'm a professional." She then pulls out an electrified Superman puppet while saying, "I hope you like electro-shock therapy and puppets!"
Harley is seen in the Tower of Fate, sitting in the Flash's cell and talking with the captured speedster. Harley is slumped against the wall as she admits she needs to talk, before mentioning the people Superman has taken from her, the Joker, Green Arrow and Black Canary. Harley admits she knows it hard's for the Flash to sympathize, "Seeing as I've strapped you to a table and electrocuted you a bit."
Harley then admits that she's made so many mistakes that she's afraid there's no one left who believes in her, before rising back up as Zatanna arrives to inform her that it's time for them to go. Harley thanks the Flash for listening to her. "I know you don't really have a choice but it means a lot." Harley says with a smile, before adding, "I may just have to keep you strapped down here forever."
Shortly after, Harley and Zatanna arrive at Jason Blood's home, where the Insurgency has gathered along with some powerful magic users. When Harley sees John Constantine and asks Zatanna who he is. When Zatanna tells Harley his name, Harley comments, "He's pretty." When Zatanna warns her that Constantine is dangerous, Harley just says, "Now he's prettier." Harley is silent through the meeting and witnesses the Spectre's attack and murder of Jason Blood and Harvey Bullock.
Harley is the first to realize Detective Chimp has been injured as she shouts, "The monkey is down!" Both Harley and Alfred check on the chimp, with Alfred confirming that he's alive while Harley adds that his breathing is shallow before picking up Chimps fallen hat and saying, "And his hat fell off." Harley is among the group that is teleported back to the Tower of Fate by Zatanna while Batman distracts the Spectre.
Harley works with Alfred and Zatanna to keep Detective Chimp alive. Realizing they main soon lose him, Harley notices Chimp is regaining consciousness before telling Alfred they have to stop his bleeding. While Alfred looks to Zatanna, Harley has Chimp squeeze her hand, an act she immediately regrets, though she's pleased he still has "crazy-strong monkey-grip". Before the three can do anything else, they realize Rose Constantine has been watching them when she announces her presence by asking, "Will the monkey be okay?"
Before Harley can respond, Doctor Fate teleports into the room, hoping to take Rose back to the upper portion of the tower. Harley calls after him, asking him to wait before pointing to Chimp and proclaiming, "I need your help here, Doctor!" putting emphasis on the first part of his name. Harley is surprised when Fate reveals he's not that kind of doctor before demanding to know what sort of doctor he is.
Fate only responds that it's complicated and Harley snaps, "We don't have time for complications. A good, talking chimp is dying! Can you help or not?"
Fate takes a long look at Chimp before declaring that he is too far gone for his abilities to be of use. Unimpressed and annoyed, Harley snaps, "Wow, that's some positive talk in front of the patient." Kneeling in front of Rose while smiling gently, Harley tells her, "Don't worry, random little girl. I've never lost a monkey before and I'm not about to start today!"
Returning her attentions to Chimp, Harley points Fate out while saying, "And you. You can't just put on a helmet and a cape and call yourself doctor. Some of us went to medical school and earned our title. Now, please take this small girl out of my operating room, 'Mister' Fate."