Over his 82-year crime-fighting career, Batman has had all manner of adventures. The quality and importance of these tales may vary, but for good or bad, they are usually complete.
DC Comics' continual need to reboot their universe means that there have been stories that are either never finished or removed from canon. Usually this is a way of cleaning the timeline up or making continuity more palatable for modern audiences. The other mechanism for removing such troubling stories from continuity is to ret-con them. See Spider-Man: One More Day as a particularly poorly executed example of this.
In the mid-2000s, various writers and editors working on the Bat-Family of titles, either deliberately or not, weaved a massive story of corruption within the GCPD into the meta narrative of the line. Members of Batman's huge supporting cast were moved around the board, positioned in opposition to Commissioner Atkins and his rotten-to-the-core police force. Then Infinite Crisis moved the timeline of the DC Universe one year ahead.
Fans would learn the story's outcome in a couple of lines of throw-away dialogue, leaving a massive untold Batman story in its wake.
7. Officer Down
As long as there has been a Batman, there has been a Commissioner Jim Gordon. Over the years, the two men have been everything from mortal enemies to brothers. Regardless of where the two stood regarding one another, they would always share a belief in justice and that one man can make a difference.
In No Mans Land's aftermath, a new Gotham is born, and Batman and Gordon's relationship is on solid footing. With the support of the GCPD behind him, Bruce Wayne wages his war against crime in a city, trying to rediscover who she is and just what has slipped between the cracks of the cataclysmic earthquake.
During this relative peace and uncertainty, Jim Gordon is shot three times in the back, forcing him to retire from active duty. Batman takes the news of his long-time allies shooting poorly and is less than impressed by the mayor's hand-picked replacement: Michael Atkins. This new commissioner carries a much dimmer view of vigilantes in general and Batman in particular than his predecessor.