Batman #677: a bunch of pieces of the puzzle flying out all at once. Some of the more obvious theories are broached: is Jezebel Jet an enemy? Is Batman suffering from multiple personality disorder and trying to destroy himself? The file that Sheldrake gives to Gordon is very interesting, and of course the biggest question is whether it's a plant or if it's actually all true, if the Wayne household was in fact far less idyllic than Bruce has always remembered it.
[spoiler]Could Thomas still be alive? Doubtful. Could this be an act of revenge by some heretofore-unknown member of Martha's family? Perhaps.[/spoiler]
There's another possibility that occurs to me:
Alfred.
He knows Bruce better than anybody, he has access to all his resources, and has his full and complete trust. And here's where the Morrisony obsession with old continuity comes in: he's gone rogue before.
Wiki:
Ironically, Alfred's loyalty would lead him to become a member of Batman's rogue's gallery. While pushing Batman and Robin out of the way of a falling boulder, Alfred was seemingly killed in Detective #328 (June 1964). It was revealed in Detective #356 (October 1966) that he had been revived by a scientist named Brandon Crawford. His attempt at regeneration resulted in a dramatic change: Alfred awoke from his apparent death with pasty white skin with circular markings, superhuman powers, including telekinesis, and a desire to destroy Batman and Robin. Calling himself The Outsider, he indirectly battled the Dynamic Duo on a number of occasions, using others as his puppets – the Grasshopper Gang in Detective #334, Zatanna in Detective #336, and even the Batmobile itself in Detective #340 – and generally only appeared as a mocking voice over the radio. He did not physically appear in the comics until Detective #356, when he is bathed again in the rays of the regeneration machine during a struggle with Batman, and returns to normal, with no memory of his time as a supervillain. His time as the Outsider is put together in Showcase presents: Batman Volumes 1 & 2.
The more I think about it, the more sense it makes. It jibes with Sheldrake's comments: "He's an ACTOR! Guess he fooled you too, Gordon, just like he did the WAYNES." He also throws out the Pennyworth/Beagle duality. Best guess is that Alfred, not Batman, is the one who's been hiding a split personality.
I think that last page means more than it appears to.