Warning: spoilers ahead for Batman #100!
The Joker War has reached its epic conclusion, and the relationship between the Batman and the Joker will never be the same. After one of the most important battles of their lives, Batman has made the decision to shift a status quo that has essentially been a constant in the DC Universe since its beginning. The Dark Knight is choosing to no longer play by the Clown Prince of Crime's rules, and by issue's end, both of them know it.
In Batman #100 from James Tynion IV with art by Jorge Jimenez, Batman has come to Joker, who's been waiting for him at ACE Chemicals, the Joker's "birthplace." As they fight, Joker has made sure to torment Batman in the darkest ways possible. Not only did he dig up and reanimate the corpse of Bruce's butler and surrogate father Alfred, but he's also wearing the shining bat suit that had been made for the as yet intangible time when Batman might one day save Gotham, his crusade against crime largely fulfilled. However, Joker's been trying to make the point all this time that Batman will never get his happy ending, that Gotham hates him, preferring to be as corrupt and dark as it's ever been.
But with all the death, destruction, and chaos that Joker's caused, Harley Quinn herself is determined to make sure that Batman changes the long-running game. Near the end of their fight, and with the entire factory on fire, Harley enters the scene, shooting one of Joker's eyes out. She straps Joker to a bomb and attaches one to herself, forcing Batman to make a choice. He can ether save her or save the Joker, who will no doubt escape prison yet again to cause more mayhem, pain, and suffering. As she leaves, Batman makes his decision. He exits the burning factory after her, leaving Joker behind.
While Batman knew there was still a chance for Joker to save himself from the resulting explosion, he still allowed for the risk that Joker could have died in ACE Chemicals. In the past, Batman would've made sure to get Joker to safety, but Joker War has changed things. Joker has pushed and exceeded the limits, as evidenced here. Batman has changed the game, and he'd now clearly be able to live with himself if Joker were to die. That doesn't mean that Batman would ever kill Joker, but Joker can no longer count on their cyclical pattern like he used to. He went too far this time.
Batman's move here is completely justified. For too long, Joker has brought insane amounts of pain and suffering on Gotham City, as well as on Batman and his family. The Joker War itself was on a level that Joker had arguably never achieved before and, as a result, Batman is no longer willing to simply continue as if it were the usual Joker encounters of the past. As far as what this means for their future, it's hard to say. For now, it looks as though Joker will be lying low, biding his time and reevaluating the new terms of his relationship with Batman.
Batman #100 by James Tynion IV and Jorge Jimenez is available now.