WARNING: The following contains spoilers for Batman: Three Jokers #3, by Geoff Johns, Jason Fabok, Brad Anderson, and Rob Leigh, on sale now.
The DC Black Label Three Jokers series finally explained the Joker's various personas and how he has survived so long in the DC Universe, despite his constant flirtations with death. While this series might not remain cannon, it does answer several questions about Joker's place in Batman's world.
Upfront, three different Jokers made Batman's life a living hell for so many years. There was The Criminal Joker, which was the original from the Golden era of Batman comics, and one who made several appearances later. There was The Clown, which was the Joker from the '70s and '80s, and the one who murdered Jason Todd. Finally, The Comedian was The Killing Joke version of the Clown Prince of Crime. By the end, there was only one Joker remaining.
In the second issue, Jason Todd got his revenge by killing The Clown, avenging his own death, much to Batman and Batgirl's chagrin and disappointment. Then, in the third issue, The Criminal tried to create a new Joker in Joe Chill, but failed and then The Comedian put a bullet in his head, killing the original Joker and heading to Arkham Asylum as the last Joker standing. Most interesting is that Three Jokers tied in almost perfectly with The Killing Joke in more than one way. While Barbara Gordon returned as Batgirl in the New 52, the fact she was Oracle remained a part of history. Commissioner Gordon found somewhere that could do specialized treatment and helped her not only regain the use of her legs but made her as good as new so she could become a superhero again. This means that, while Barbara can walk and fight again, she still suffered the gunshot that paralyzed her by Joker. In that case, it was The Comedian, the one Joker that survived. That is why Barbara and Jason were the two working with Batman in Three Jokers.
This shooting in the pages of The Killing Joke by Alan Moore, Brian Bolland, and Richard Starkin. It started with Batman paying a visit to Joker, trying to talk to him to let him know he didn't want their battle to end with one of them dead. However, he learned Joker had broken out of Arkham Asylum, and the story moved to Joker's point of view, with the Clown Prince of Crime and his memories of his past. Joker remembered when he was married, and his wife was pregnant, and that he was a comedian, trying to get a gig. When his wife seemed disappointed he didn't get the gig, he lost his temper, and it was because he clearly was unsure of himself. He finally broke down, crying, and his wife comforted him. He admitted he wanted to set them up for a better life, and she was there to let him know she was there for him and was behind him. He then met with some local gangsters and agreed to help them pull off a crime. The police showed up, took him outside, and told him his wife had died. That night, he took the job and became Joker after Batman busted up the robbery.
In the final issue of Three Jokers, Bruce Wayne brought that story back to the forefront. He told Alfred he knew the Joker's identity one week after he met him. It wasn't the Criminal or the Clown that Batman meant, as their identities remain a mystery. Batman confirmed that Joker's origin from The Killing Joke was the real origin for The Comedian, with one twist. His wife didn't die, as the police helped her fake her death and sent her into hiding in Alaska.
Bruce said no one needs to know Joker's real name because his wife and child need to remain anonymous and protected. The Comedian became Joker because his wife escaped from him and the GCPD helped her do it. Batman now protects her from her ex-husband's sins at all costs.