This Dark Knight was a clone of Bruce Wayne created by Darkseid. The Batman's apparent death occurs in Final Crisis #6 when he confronts Darkseid. Batman announces that he will break his "no gun" rule while facing Darkseid. Wielding a sidearm made on Apokolips, Batman shoots Darkseid in the chest with a bullet made of Radion (the same bullet used to kill Orion), just as Darkseid unleashes his Omega Sanction, or the "death that is life", upon Batman. However, the Omega Sanction does not actually kill its target, but sends its consciousness into parallel worlds. Although the presence of Batman's corpse would suggest that he is dead, at the conclusion of Final Crisis it is revealed that Batman has been sent to the distant past, and it is later revealed that the corpse assumed to be Wayne's was in fact that of Darkseid's clone.
Grant Morrison's 2008 storyline, Batman R.I.P., featuring Batman being physically and mentally broken by the enigmatic "Black Glove," garnered much news coverage in advance of its highly-promoted conclusion, which would supposedly feature the death of Bruce Wayne. The original intention was, in fact, not for Batman to die in the pages of "R.I.P.," but for the story to continue with the current DC event Final Crisis and have the death occur there. As such, a two-issue bridge arc was designed called "Last Rites" that showed Batman survive his helicopter crash into the Gotham City River and return to his Batcave, only to be summoned to the Hall of Justice by the JLA to help investigate Orion's death. This in turn led into the events of "Final Crisis" (which began publication while Batman R.I.P. was concluding), where Batman is kidnapped by Granny Goodness. "Last Rites" told the tale of Batman being mentally probed by Darkseid's minions Mokkari and Simyon, in an attempt to cull the personality traits that make Batman the successful super-hero that he is in order to transplant them into cloned bodies. The plan fails due to the clones, imparted with Batman's memories and thoughts, "clawing out their own eyes." Mokkari wonders aloud, "How does Batman process this degree of stress?" and "What kind of man can turn even his life memories into a weapon?"
The two-parter concludes with a major "Final Crisis" plot point, as it is revealed that Batman kept a bullet made of Radion (that was used to kill Orion) in his utility belt. In Final Crisis #6, Darkseid is in his bunker with Batman. He attempts to sneak up on the villain, but Darkseid tells him to just come out of the shadows. Batman reveals himself, commenting that Orion did more damage to Darkseid than he realized. Unfortunately, he's dragging the Earth with him, and will destroy it unless stopped. Despite Batman's vow about firearms, this is too great: Batman is going to use a gun to fire the same bullet Darkseid used to kill Orion. He states specifically to his former master that he will make an exception to his "no firearms" rule before raising his pistol. Darkseid asks if he can outrace the Omega Sanction, but Batman fires anyway. The bullet hits Darkseid in the shoulder as he fires the Omega Sanction from his eyes, hitting Batman.
Before the Omega Sanction hits Batman, he silently says, "Gotcha". (Morrison notes that Batman's use of the gun is symbolic as “the root of the Batman mythos is the gun and the bullet that created Batman. So, Batman himself is finally standing there to complete that big mythical circle and to have the image of Batman up against the actual personification of evil and now he's got the gun and he's got the bullet. It seemed to me to work.") At the close of the penultimate issue in the series, Superman returns to Earth from the 31st century, where he was given access to the reality-altering Miracle Machine by Brainiac 5 of the Legion of Super-Heroes. In a fit of desperate rage, Superman attacks Darkseid's bunker, unleashing a massive blast of heat vision on the intergalactic headquarters. Inside, he discovers the smoking corpse of one of Darkseid's Bat-Clones, believing it upon examination to be that of his real friend.
As Superman gently carries the clone's body, Darkseid mocks the Man of Steel for failing to defend Earth, and that as Darkseid has becoming everyone and everything, Superman is now the enemy of all that lives. Driven to a rage, the Man of Steel is about to tear the Dark God apart when he realizes that Darkseid is in the body of Dan Turpin. Darkseid declares that the Final Crisis is over, and he has won, preparing to fire the Radion bullet which will kill Orion in the past. Speaking through Turpin and his Anti-Life slaves, Darkseid asks if Superman will join Batman in the Omega Sanction, or try and outrace it. Superman refuses to give in to Darkseid, and tells him its not over yet. Just then, Barry Allen and Wally West arrive, leading the Black Racer to the dying Darkseid. The Anti-Life slaves unleash Omega Beams on the two Flashes, who outrace them, run past Superman (who is naturally surprised by Barry's presence) and vibrate through Darkseid. Having just fired the Radion bullet, Darkseid panics at the sight of the Black Racer, who claims Darkseid's soul, removing him from Turpin's body.
Superman later returned the clone's remains to Nightwing and Robin, to be left in a memorial similar to the one Batman made for Jason. At Alfred's insistence, no public funeral was held for Batman, and Robin, refusing to believe he had been killed, prevented them from declaring Bruce Wayne dead. The charred clone was buried in an unmarked grave next to Thomas and Martha Wayne.
Some weeks later, as Gotham City was going through a rampant crime wave following Batman's disappearance, Green Lantern Hal Jordan and Barry Allen, the second Flash, who had returned during the Final Crisis, met each other at the Bat-Clone's grave for a private farewell to their friend. They reflect on Batman's apparent death and how the hero community is avoiding linking Wayne and Batman. Barry reminded Hal that they, Superman, and Green Arrow all died and returned, and if anyone could beat death, it was the Dark Knight. The conversation moves on to the world becoming "more dangerous" after Barry's death and observing that the deaths of Arthur Curry and J'onn J'onzz cost the Justice League its "heart and soul". As they leave the cemetery, Barry expresses hope that their dead comrades will be returned to them. He specifically cites Batman again noting, "If there's an escape, you can bet Batman's already planning it."
Unfortunately, soon after they left, the criminal Black Hand arrived in the cemetery, approaching the unmarked grave of the Batman clone, saying "Yes. This one." He then pushes his hand through the ground in front of the headstone and forcibly extracts the clone's skull. He begins to recite the Black Lantern oath:
"The Blackest Night falls from the skies the darkness grows as all light dies we crave your hearts and your demise by my Black Hand - the dead shall rise!"
Black Hand languishes with the Bat-Clone's skull, talking to it and insisting that it will play a vital part in the events to come. While reciting the oath, Black Hand's ring begins to glow and swirl as light shines in the eyes of the skull he is holding. While holding the skull, Black Hand tells the mysterious force behind the Black Lanterns (residing in Sector 666) that no one escapes death. He is later seen after Black Lanterns Elongated Man and Sue Dibny kill Carter Hall and Kendra Saunders. Hand enters the room and proclaims that Hawkman and Hawkgirl will not escape death this time. Two black rings fly out of the Batman clone's skull and Hand commands the two fallen heroes, by name, to rise. Soon after, Alfred Pennyworth makes his way to the grave of the deceased clone. He discovers Black Hand's raid of Batman's unmarked grave, and goes to alert the Justice League. Black Hand subsequently recruits the skull into the Black Lantern Corps. When Barry Allen attempts to attack Nekron, Black Hand steps in, using the clone's skull as an "emotional tether" to weaken the hero.
The head Black Lantern, Nekron, later uses a Black Lantern Ring to resurrect the Batman Clone as a Black Lantern and build it a form to tether an emotional connection to the heroes present and has it spit out Black Lantern Rings that attach themselves to heroes that have suffered apparent death in the past: Superman, Wonder Woman, Green Arrow, Superboy, Kid Flash, with two more failing to reach Flash (Barry Allen) and Hal Jordan. The skull of the clone reconstructs it's body to move against the Justice League and the Titans.
After the Black Lantern clone had created several black power rings to attach to and kill the majority of the Justice League, the skull began to return to normal after Nekron explained it had served its purpose. Nekron also referred to the skull as "Bruce Wayne", knowing that the body was not authentic. Almost immediately after, much to everyone's surprise, Nekron completely releases the skull from the Black Lantern ring.
Dick Grayson was able to get hold of the clone's skull and body after these events of Blackest Night, locking it into a vault, lest it be further defiled. The vault requires a password to be opened: "Zur En Arrh", a repeated phrase in the Batman comic series.
Later, Jason Todd observes to Dick that if a Lazarus Pit can resurrect him, it can do the same for Bruce Wayne. At Todd's behest, Dick immersed the Batman clone's body in a Lazarus Pit, hoping to revive his seemingly dead mentor. The clone is resurrected in Batman and Robin's third storyline, "Blackest Knight," but its memories are warped and unstable. Having been buried and killed once by Darkseid, then resurrected as a Black Lantern, before returning to lifelessness again, drives the clone mad. A team of Batwoman, Dick Grayson, The Squire, and The Knight gathered to watch the resurrection of Batman were surprised to be met by a fierce, mindless combatant. After attacking Damian Wayne, the clone burns out and dies for the final time. Grayson then realized the truth about Batman's corpse, coming to the correct conclusion that it had been a fake. Dick finally accepts that Bruce Wayne is still alive somewhere.
Morrison's storyline continues with the miniseries Batman: The Return of Bruce Wayne. In the miniseries, Bruce will travel through time from the prehistoric era back to present-day Gotham City.