This story runs through issues #8-12, and into Annual #1 of the New 52 Batman comic, all collected as Batman Volume 2: The City of Owls HC (The New 52)
. It is continued from the previous volume Batman Volume 1: The Court of Owls TP (The New 52)
, which collected issues #1-7. It is a direct continuation of the first volume, as the Court of Owls unleashes their army of zombie ninjas on Gotham, hitting Wayne Manor and the Batcave with one force, while another goes off to assassinate the City's top officials. Luckily, the Bat-family are available to handle the assassins, while Batman and Alfred hold the fort at home. Did you ever wonder what the big dinosaur trophy was for?
Now, this crusade against the Owls is interrupted by Mr Freeze's escape from Arkham - I'm not sure exactly why (the interruption that is, not Mr Freeze's reason for escaping) - but soon Batman is on the trail of the Court of Owls, only to find someone has beaten him to the kill, and that someone turns out to be both the person we all assumed would be the baddie as soon as we set eyes on him (well, I did), and who turns out to be Bruce Wayne's long lost secret [spoiler] - and its not his dog either, that's over in Batman and Robin volume 1... Anyway there is a big climactic showdown that reveals deep, dark secrets before it all ends in big explosions.
As a follow-up, we also get a look at Alfred's father, Jarvis's career with the Waynes, and his part in the secret history.
This story didn't really work for me, probably because the first volume didn't work, and seemed to be rehashing old ideas and stories. However, that might just have been me having a bad day.