After the 12-issue limited series Crisis on Infinite Earths, DC Comics rebooted the histories of some major characters in an attempt at updating them for contemporary audiences. Frank Miller retold Batman's origin in the storyline Year One from Batman #404-407, which emphasizes a grittier tone in the character. Though the Earth-Two Batman is erased from history, many stories of Batman's Silver Age/Earth-One career (along with an amount of Golden Age ones) remain canonical in the post-Crisis universe, with his origins remaining the same in essence, despite alteration. For example, Gotham's police are mostly corrupt, setting up further need for Batman's existence. While Dick Grayson's past remains much the same, the history of Jason Todd, the second Robin, is altered, turning the boy into the orphan son of a petty crook, who tries to steal the tires from the Batmobile. Also removed is the guardian Phillip Wayne, leaving young Bruce to be raised by Alfred. Additionally, Batman is no longer a founding member of the Justice League of America, although he becomes leader for a short time of a new incarnation of the team launched in 1987. To help fill in the revised backstory for Batman following Crisis, DC launched a new Batman title called Legends of the Dark Knight in 1989 and has published various miniseries and one-shot stories since then that largely take place during the "Year One" period. Various stories from Jeph Loeb and Matt Wagner also touch upon this era.
In 1988's "Batman: A Death in the Family" storyline from Batman #426-429 Jason Todd, the second Robin, is killed by the Joker. Subsequently Batman begins exhibiting an excessive, reckless approach to his crime fighting, a result of the pain of losing Jason Todd. Batman works solo until the decade's close, when Tim Drake becomes the new Robin. In 2005 writers resurrected the Jason Todd character and have pitted him against his former mentor.
Many of the major Batman storylines since the 1990s have been inter-title crossovers that run for a number of issues. In 1993, the same year that DC published the "Death of Superman" storyline, the publisher released the "Knightfall" storyline. In the storyline's first phase, the new villain Bane paralyzes Batman, leading Wayne to ask Azrael to take on the role. After the end of "Knightfall", the storylines split in two directions, following both the Azrael-Batman's adventures, and Bruce Wayne's quest to become Batman once more. The story arcs realign in "KnightsEnd", as Azrael becomes increasingly violent and is defeated by a healed Bruce Wayne. Wayne hands the Batman mantle to Dick Grayson (then Nightwing) for an interim period, while Wayne trains to return to his role as Batman.
The 1994 company-wide crossover Zero Hour changes aspects of DC continuity again, including those of Batman. Noteworthy among these changes is that the general populace and the criminal element now considers Batman an urban legend rather than a known force. Similarly, the Waynes' killer is never caught or identified, effectively removing Joe Chill from the new continuity, rendering stories such as "Year Two" non-canon.
Batman once again becomes a member of the Justice League during Grant Morrison's 1996 relaunch of the series, titled JLA. While Batman contributes greatly to many of the team's successes, the Justice League is largely uninvolved as Batman and Gotham City face catastrophe in the decade's closing crossover arc. In 1998's "Cataclysm" storyline, Gotham City is devastated by an earthquake. Deprived of many of his technological resources, Batman fights to reclaim the city from legions of gangs during 1999's "No Man's Land." While Lex Luthor rebuilds Gotham at the end of the "No Man's Land" storyline, he then frames Bruce Wayne for murder in the "Bruce Wayne: Murderer?" and "Bruce Wayne: Fugitive" story arcs; Wayne is eventually acquitted.
DC's 2005 limited series Identity Crisis, reveals that JLA member Zatanna had edited Batman's memories, leading to his deep loss of trust in the rest of the superhero community. Batman later creates the Brother I satellite surveillance system to watch over the other heroes. Its eventual co-opting by Maxwell Lord is one of the main events that leads to the Infinite Crisis miniseries, which again restructures DC continuity. In Infinite Crisis #7, Alexander Luthor, Jr. mentions that in the newly rewritten history of the "New Earth", created in the previous issue, the murderer of Martha and Thomas Wayne – again, Joe Chill – was captured, thus undoing the retcon created after Zero Hour. Batman and a team of superheroes destroy Brother Eye and the OMACs.
Following Infinite Crisis, Bruce Wayne, Dick Grayson, and Tim Drake retrace the steps Bruce had taken when he originally left Gotham City, to "rebuild Batman". In the "Face the Face" storyline, Batman and Robin return to Gotham City after their year-long absence. Part of this absence is captured in during Week 30 of the 52 series, which shows Batman fighting his inner demons. Later on in 52, Batman is shown undergoing an intense meditation ritual in Nanda Parbat. This becomes an important part of the regular Batman title, which reveals that Batman was reborn as a more effective crime fighter while undergoing this ritual, having "hunted down and ate" the last traces of fear in his mind.
At the end of the "Face the Face" story arc, Bruce adopts Tim as his son. The follow-up story arc in Batman, "Batman & Son", introduces Damian Wayne, who is Batman's son with Talia al Ghul. Batman, along with Superman and Wonder Woman, reforms the Justice League in the new Justice League of America series, and is leading the newest incarnation of the Outsiders.
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 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. However, out of desire to give the storyline of "R.I.P." a suitable conclusion in an of itself, Batman appeared to die in the final chapter of the story, only to turn up alive in the very next issues as a prisoner of "Crisis" villain Darkseid. The death came a month later, in the limited series Final Crisis, during which Batman confronts the story's villain Darkseid. Making rare exception, Batman uses a gun, loaded with a Radion (which is poisonous to the New Gods) bullet, to shoot Darkseid's shoulder, just as Darkseid unleashes his Omega Sanction, the "life that is death", upon Batman and his charred corpse is recovered by Superman. However, the Omega Sanction does not kill its victims: instead, it sends their consciousness travelling through parallel worlds, and at the conclusion of Final Crisis, it is made clear that this is the fate that has befallen the still-living Batman, as he watches the passing of Anthro in the distant past.