Before Arkham City Incident
After the Arkham Asylum Incident, Joker was suffering from a horrible side effect of the Titan Formula, which gave him a fatal disease that was progressively killing him. When Mr. Freeze was released into Arkham City, Joker blackmailed Freeze into making the cure by threatening his wife, Nora's safety. Before Freeze could completely finish the cure, Hugo Strange was able to manipulate him , stripped him of his suit and weapons, and gave him to the Penguin who stole his Freeze Gun afterwards and kept him prisoner at The Cyrus Pinkney Institute for Natural History.
Arkham City Incident
Batman came to Arkham City to investigate Strange's plan, and began to track Joker to see what he knew about Strange's scheme, Protocol 10. Batman eventually found Joker, but arrived to see his seemingly lifeless body in a wheelchair, with Harley Quinn crying over him. Batman approached Joker's body and used Detective Mode to scan his body, but was ambushed by another "Joker" who gassed him and was knocked unconscious by Harley with a Baseball Bat. When Batman woke up, he found himself tied up to the wheelchair. Joker approached Batman and told him that he was dying of the Titan Disease and that he had infected him with his blood, which gave Batman the disease too. Batman told Joker that he was fine with the two of them both dying, but Joker informed the latter that he had shipped samples of his blood all over Gotham. With no other option, Batman agreed to search for Joker's cure and prepared to find Mr. Freeze since he's already working on the cure.
Batman found Freeze in Penguin's clutches. Batman asked Freeze how he could stop Penguin who was still using his Freeze Gun. Freeze told Batman that there's a special override chip in his suit for that special occasion. Batman used the chip and defeated Penguin, even when Solomon Grundy was on his side. Freeze admitted to Batman that the cure he made wasn't completely finished. The problem was that his cure degraded too quickly to be used, and required required a restorative enzyme. Batman realized the restorative enzyme element that was needed could be found in Ra's al Ghul's blood.
After Batman required Ra's blood sample, Freeze was able to complete the cure and made two vials of the antidote. Batman demanded the cure, but Freeze refused, and destroyed one of the vials and stored the other in his safe. Freeze told Batman that since Joker still had his wife, he would only give him the cure if he managed to return Nora to him. Batman and Freeze engaged in a fight, and Batman was able to defeat him and opened the safe, but Harley Quinn was able to break into the safe and stole the other vial.
Harley Quinn was ambushed by Talia al Ghul, who stole back the cure for Batman. Batman returns to the Sionis Steel Mill and found Joker who appeared to be "cured". When Batman was about to take down Joker, they were interrupted by Strange's Protocol 10. In the explosion, Batman got pinned down by piles of rubble, which gave Joker the opportunity to kill him. Talia arrived just in time to save Batman and gave Joker the chance to get immortality through the Lazarus Pit. Catwoman eventually found Batman and helped him out of the rubble. After Batman stopped Hugo Strange from completing Protocol 10, he tracked Joker and Talia down to the Monarch Theatre.
Batman found Joker holding Talia at gunpoint and demanding the cure, which left him bewildered: he believed that Joker already had the cure. With the confusion, Talia stabbed Joker in the back and revealed that she had the cure. Batman looked at his enemy's body, believed that his death was an unnecessary casualty, and told Talia that there was always an alternative tactic to defeating an enemy. Talia defended her course of action to Batman by stating that it was a necessary one in order to save him, comforted him, and assured him that the long night of chaos and destruction instilled by the Joker, Hugo Strange, and her father, was finally over.
As Batman thought back to what happened earlier that night, he realized that Joker had never actually received the cure, and that the Joker that Talia had killed was actually a decoy. The real Joker shot Talia in the back before Batman could react and she died in his arms. The Joker decoy was revealed to be Clayface, who prepared to kill Batman so he could assume his identity as "The role of a lifetime". Batman eventually defeated Clayface and drank half of the antidote, which cured him of the Titan Disease. Joker tried to save his own life by using the Lazarus Pit, but Batman destroyed the machine by using Talia's sword.
With his plans ultimately ruined, Joker demanded his last hope from Batman, and taunted him that despite all the death and destruction that he caused in just a single night, Batman would still save him. Batman voiced his hatred of the Joker and his temptation to refuse him the cure and let him die, and knew that he would only continue to break out and kill if he was left alive and locked up. Laughing at the absurdity of their never ending battle, Joker stabbed Batman in the arm, which caused him to drop the vial, and shattered on the floor. Joker screamed in horror as Batman threw him to the ground and tried in vain to drink the cure from the floor. With Joker having only seconds of life left, Batman told his nemesis that he would've still saved him in spite of everything that he did. Seeing this as genuinely funny, Joker decided to laugh as he took in his final breaths and died with a smile on his face with Batman looking down at him in silence.