Batman: Endgame is a six issue comic and takes place after the story lines of the Batman Eternal series, and brings the joker back from the Death Of The Family series.
In the first issue of the series the scarecrow unleashes a fear inducing chemical attack on Gotham, making almost everyone go mad. Batman then gets attacked by the justice league under some other kind of mad chemical not yet known,
he then puts on a suit he calls "Fenrir," a suit he made in the past to take on the whole justice league if need be, while in"Fenrir" he is able to defeat and subdue Wonder Woman, Aquaman,and the Flash. Then out of know where he is attacked by Superman and thrown around Gotham for a little while, Batman then gets the upper hand and asks Superman who or what turned him and the rest of the justice league against him and Superman just begins to laugh along with all of the other justice league uncontrollably.
Superman then attacks Batman again but not for so long because Batman subdues him with Kryptonite gum. He then figures out that the whole justice league was injected with a super powerful form of the joker toxin that was customized for each league member. Knowing that the joker is behind this Batman revisits the jokers old cell back at Arkham Asylum and meets Eric Border. Border then tricks Batman and locks him in jokers old cell only to reveal behind bars and makeup that he was the joker all along by using different drugs to mask his appearance.
With Batman locked up the joker then decides to tell him that he will be truly helpless as his master plan begins and that he and Batmans relationship will come to a permanent end, then fills the cell with a type of a paralytic gas.
Batman wakes up to to hearing Julia telling him that the joker has unleashed an unknown airborne pathogen that has taken over Gotham and makes the people of Gotham look like the joker and is transmitted by laughter. Batman now free from the jokers old cell heads to the Gotham Presbyterian hospital where Julia tells him that that was the first reported place of outbreak and there he finds a crazy disfigured infected Joe Chill (the man that murdered his parents) and a recreation of one of Batmans biggest heartbreaking moments, the night his parents died.
Joe then tells Batman that the joker knows his true identity. Meanwhile Jim Gordon researches some old Gotham records and finds pictures of the joker decades before his first confrontation with batman, all of the sudden Jim is attacked by the joker and in a flash Jim shoots the joker dead, then in panic he calls Batman to tell him what happened, but the joker rises behind Jim and knocks him out, while Batman is yelling for Gordon the joker picks up the phone and responds...."Hello, Bruce."
Batman bursts in James's house and finds Jim dying with an axe in his chest, then realizes that Jim is infected by Jim suddenly jumping up and attacking him
, With Julia and Nightwings help they subdue Jim, and Batman realizes that the joker might have made a cure to aid in the almost fatal damage and that in that cure he and Alfred could run a complete inverse of the cure or infection. Julia then tells Batman that Paul Dekker was released around a year ago so he tracks him down and confronts him. Dekker tells Batman that was able to develop a healing serum and virus using a component from only the jokers spine, Dekker also tells him that after all of his research he thinks that the joker is immortal. When Batmans back is turned Dekker injects himself with another serum that was given to him by the joker thinking it would make him immortal and it kills him in a matter of minutes, after Batman witnesses this he then hears from Julia and she tells him that she has done a search around Gotham and found some images of the joker through the past few centuries of Gotham history, she also tells him that if he doesn't find a cure in the next twenty four hours that everyone that has been infected will die.... he then turns to the court of owls for some possible help.
The court of owls decide to not help Batman out with this as it does not concern them, Batman then angered confronts Uriah Boone (who has been around since the beginning of Gotham) asking him if he knows anything about the joker being immortal or not. at this time the joker swims to the Batcave and Alfred realizes that the Batcave has been breached and decides to take matters into his own hands, but before he knows it the joker cuts his hand off and steals some of Batmans trophies.
A few hours later the joker hosts a parade throughout Gotham and all of its infected citizens with floats bearing the trophies he stole from Batmans cave. With no other choice Batman decides to get not only his crime fighting family but also some of his greatest supervillains together to save whats left of the city. after the joker hears about his new team he begins to prepare for the "best trick of all."
in this last issue of the series it starts with some of Batmans new allies being taking down by the jokers lethal gas. Batman and the joker start to finally fight and the joker breaks Batmans mask and realizes that it was Nightwing in Batmans suit as a distraction while the real Batman was searching a cave under Gotham that the joker fell through during the "Death of the Family" story line, he then realizes that a part of the cave was rigged with the jokers explosives, the part rigged with explosives had a big pool of dionesum (the fluid that makes the jokers healing factor super advanced) under them. With the joker knowing what batman was up to he sets the explosions off and the joker travels his way down through the tunnels himself. As the cave is collapsing the joker and Batman begin to fight, during the fight batman breaks the jokers back and the joker sticks two knifes in batmans back. Joker then tries to make his way to the big pool of dionesum, but batman stops him just before a part of the cave comes crashing down destroying the dionesum, Batman then tells the joker that he had failed because he had given all of his allies a small dose of the dionesum to protect them from the poison and gave Julia another big piece of it to cure the city. Batman and the joker lay wounded on the cave floor and the cave finally collapses on them killing then both.
A few days later it shows Alfred in the hospital with Julia at his side refusing to have his hand reattached because he had no use for it seeing that he had no one to cater for anymore. Julia then tells him that the city is finally cured due to the dionesum and asks Alfred if he wants to take a look at Batmans final letter, he denies first then after thinking a bit decides to read it and all it says is "Ha."