The Joker and Harley Quinn had been planning a new scheme for weeks, and it was finally time to strike. Nightwing, Dick Grayson, had already left to establish himself away from Gotham, in another city. By that time, it was only Bruce Wayne as Batman, Barbara Gordon as Batgirl, and Tim Drake as Robin.
On a night when Robin was alone, Harley dressed up as a woman in the need of help, who was about to get beaten by two men in an alley. After Robin saved her by knocking out the two, she ambushed him with a giant mallet. Joker and Harley took them back to their new home, the old Arkham Asylum, which had been torn down and all the current inmates were sent to a different location.
Batman and Batgirl tried to find the whereabouts of their friend, calling on each and every criminal of Gotham. For three weeks, nothing had been seen. On rooftop of a building, a clown which had a grenade inside exploded, letting an Arkham straight jacket fly into the hands of Batman.
Knowing that the kidnapper was at Arkham, Batman and Batgirl rushed to the rundown asylum. As the scanned the area, they found Joker and Harley in the kitchen area. Batman quickly asked where Robin was, and the only answer they gave was that they had no clue where Robin was, but they might have meant their Little J. Joker and Harley noted they decided to adopt a child rather than going through child birth and then revealed to Batman that their J.J was none other than Robin, Tim Drake. To Batman's shock, he lunged after the Joker, chasing him up the asylum.
In the meantime, Harley and Batgirl began to fight, eventually running of Arkham. When asked by Batgirl why she would commit such a crime, Harley simply answered, "Okay, so he roughed the kid up a little, but I'll make it right," since she is desperate to have the Joker's children, although she denies it when in his presence.
A fight to the finish sent both of them flying off a cliff, with Batgirl handing onto the edge and to Harley's cufflink. As she desperately tried to pull Harley up, her cufflink rips, sending Harley to fall to the bottom of the pit.
Inside Arkham again, The Joker lets Batman view their "Family Memory" tape, which shows all the tests that Robin was put through. As he was tested, Robin began to share all of Bruce's secrets because he was getting weaker. Now calling him by his real name and calling him pathetic, Batman run and attacked Joker, knocking him down. Tim entered the room again, with a gun. Joker beckoned him to shoot Batman, but instead, dropped the gun and pushed the Joker into some cords. The Joker tried to attack young Tim, but slipped on water and electrocuted himself.
Harley's body was never found, but everyone presumed that she was alive. In 2040, she comes back, paying the bail for Delia and Deidre Dennis, Dee Dee. She is their grandmother who raised the twins. Harley must have realized that the Joker was dead, moved on, and started her own family.
Interesting Fact: Harley was originally supposed to die in the Arkham flashback scene permanently, but as sneaky as our favorite Mr. Paul Dini is, he snuck Harley into the ending as Dee Dee's grandmother! Bruce Timm called Paul on the phone, telling him that Harley had to die for helping the Joker on this caper, but Paul cried, "I can't kill her! You can't make me! She's my daughter!" When Bruce read the ending, he actually liked the way it turned out, so Harley was back. Yay! We love you, Paul!
Harley with Ivy, Catwoman, Robin (yes, a female) and Batman in a Batman Beyond musical.