The third trade wraps everything up, solves the murder, and frees Bruce of his charges.
The Breakdown:
With Batman free, the Batman Family continues to investigate the circumstances of the crime. Many start to doubt Bruce's innocence, but Batgirl and Nightwing realise that infiltration of the Batcave is possible, and also realize that Vesper was methodically killed- the killer using a nerve strike to incapacitate her while beating her enough to show without it being fatal- whereas the evidence suggests it was a 'spur-of-the-moment' move on Bruce's part. At the same time, Batman launches his own, independent, investigation into his framing, and steadily uncovers a conspiracy. At the same time, a confrontation between himself, the Joker and Catwoman prompts Batman to realize how important his Bruce Wayne identity is; he moved to protect a wounded criminal because that is what his father, Thomas Wayne, would have done. An earlier meeting with the detective who comforted him after his parents' deaths serves to reinforce the importance of Bruce Wayne in Batman's life; as far as the detective is concerned, it was Bruce Wayne's life that was forever defined by the death of his parents... and the detective is also convinced that, whatever Bruce Wayne became that night, he did not become a killer.
After returning to the Batcave and apologizing for his past actions, Batman reveals to the Batman Family that the murderer is David Cain. Cain had been hired by then-President Lex Luthor to discredit Bruce Wayne for his stance against Luthor during the No Man's Land storyline; however, Cain subsequently deduced Batman's true identity- recalling his own acquaintance with a young Bruce when Bruce went to him for training- and was thus able to frame him for a crime where the only motive was Batman's desire to protect his identity. Capturing Cain, Bruce's name is subsequently cleared.
This story runs through Azrael #91, Batgirl #27 and 29, Batman #600-601, 603, and 605, Batman: Gotham Knights #27-28 and 30-31, Birds of Prey #41-43, Detective Comics #768-772, and Nightwing #68-69.