He was portrayed by Scott McClure, who is also one of the writers of the series.
After the events of The Dark Knight, the Joker was arrested and taken to Arkham Asylum. One of the people who interviewed him was a psychiatrist by the name of Harleen Quinzel. Much like in the comics, Joker takes a keen interest in her the moment she interviews him. He reveals to her that he actually likes being in Arkham and doesn't want to leave, something that interests Harleen. He also doesn't want to be in prison out of fear of his own life. One night, Joker somehow convinces one of the guards named Steve to let him out of his cell temporarilycso he can look around Harleen's office. Unfortunately, he ends up in the wrong office, and he is actually in the one belonging to Dr. Jeremiah Arkham, the asylum's owner. However, he still sticks around the office, accesses Jeremy's computer, looks up information on the internet and discovers Metropolis businessman Lex Luthor is looking for property to own, and Joker leaves a message at his headquarters for an offer and to strike up a deal, hoping to remain in the Asylum if Lex is in control. Steve arrives and attempts to get Joker back in his cell, telling him his time is up. Joker responds by bludgeoning him to death with Steve's flashlight and pours prescription pills down his throat. he later left the body in Harleen's office as a present.
At one point in the show, Dr. Hugo Strange came to Arkham and put the Joker under hypnoses in attempt to reach him. Unfortunately, Joker makes remarks about how he had been sleeping with Strange's wife while under the hypnoses, causing Strange to beat him in a fit of rage and get kicked out. Jeremiah gets Joker to sign a forum that he wouldn't take further action on the matter.
Throughout the course of the show, Joker continues to try and win Harleen's heart, but to no avail. At one point, he finds out that she's about to be married, a piece of information that would motivate him to escape. He is able to do so with the help of one of the inmates, whom he kills immediately afterwards.
He then kidnaps one of Arkham's nurses, Pearl, and puts her in the trunk of Jeremiah's car, and waits for him in the back seat. Once Jeremiah arrives, Joker forces him at gunpoint to continue driving without telling anybody (although he does manage to hint at one of the security guards that something's wrong). As he is driving, Joker forces him to go to Lyle Reeves' house. Once there, Joker hits Lyle over the head with a baseball bat, knocking him out, and kidnaps him.
Joker then takes Jeremiah back to his house, where he knocks his wife out and gags them both with duck tape, before killing their chef and tormenting them both on camera by giving Jeremiah a choice on whether to let his wife get slaughtered or cut his eyes out with a fork. Joker does neither to either of them, but instead leaves a bomb with his wife whose still tied up, then takes Jeremiah with him and drives away.
Joker forces Pearl to drive, and he takes Lyle to a sewer where he locks him in (presumably with Killer Croc) and leaves him there. They drive over to an apartment building which Joker thinks belongs to Harleen's fiance, but once he gets there, he discovers that he is in fact in the room belonging to Guy's brother, Kopski. Once Kopskis arrives, Joker knocks him out and handcuffs him in the bathtub, giving him options on how to kill himself. Joker leaves a suicide note he forged from the computer behind, forces Kopski to sign it, and throws his camera, that is still plugged in, into the tub, electrocuting Kopski and killing him. Joker leaves the apartment, and notices a homeless man watching them. He gets Jeremy to accompany him when approaching the man, who is called Theodore. He asks Theodore if he wants to die, however Theodore tells him he does in fact want to die, given he's lost both his job, his wife, and his home. So instead of killing him, Joker offers him a job to be his camera man and video him during the night. Theodore agree to this offer, thinking Joker will kill him in return.
They drive over to Harleen's wedding, and he has them stay while he goes into the church to kill Guy. He does so by shooting him in the stomach, causing all the other guests to leave in fear (with the exception of Harleen herself, and the cameraman, Jack Ryder as he's taping the incident). While Joker approaches Harleen, the lights go out and Batman appears at the Church. Joker and Jack Ryder flee into the basement, but Joker is grabbed by Batman who swears he should of let Joker die. But Batman is shot by Harleen, and Joker appears to try and flirt with her. She responds by calling him "puddin" and the shoots him in the arm. Batman disappears, and Joker attacks Jack and steals his camera (it's unknown as to what he did to him afterwards).
Joker flees the building and gets into the car. They drive to a car park, and the Joker tries to disfigure Pearl with a knife after making up a story about bullies causing his cheek scars. But the Gotham City Police Department are searching Gotham for Joker, and cars arrive at the car park. Jeremy escapes, and Joker and Theodore escape from the police by firing at them. They steal a police car, and drive around the city, and Joker captures Jeremy again who they find running across a road. The police are all over Gotham, and Joker takes Jeremy back to his street, where its only mere minutes till the bomb he left with Jeremy's wife is to explode. Joker handcuffs Jeremy to a police car and forces him to sign the asylum over to Lex Luthor. But Joker goes against his word, and makes Jeremy witness his house blow up with his wife still inside. Jeremy attempts to attack Joker, but only gets knocked out as a result. Joker gives Theodore an envelope and the tape with the night's footage on it to post on the internet, and lets him leave alive-much to Theodore's disappointment. Joker then sits next to an unconscious Jeremy, and phones the police and tells them he wants to go home, before laughing away to himself, watching the fireworks caused by the explosion.
Joker is arrested and sent back to Arkham Asylum. While in a holding cell, he is approached by Lex who is now owner of Arkham Asylum. Joker then told him that he helped him get the place and asks Lex if he is going to keep his end of the bargain. Lex replies yes, and a happy Joker shakes hands with Lex, stating "pleasure doing business with you Lex".
In the last Further Evidence titled "Therapy Ends", Dr. Quinzel, now taken the name Dr. Kopski, confronts the Joker for the first time in six months after the wedding incident. He is badly bruised because the therapy sessions (which Harleen had not been attending) have become a time for the security guards to assault the Joker. Harleen finally states that there is no fixing the Joker, that she'll give the guards a raise for what they've done and he will die down in maximum security. The episode ends as the Joker tells the guards a "joke" before they beat him.
In Series II, Joker escapes Arkham after the entire place is put under attack and kills one of the security guards. As of now, any new episodes have not yet been released, ending with Joker escaping and getting away with all he had done.