We should presume that Morrison's telling the same story he was telling with or without the DCnU reboot, give or take minor glitches (such as, perhaps, Jason Todd being free from prison; Dick Grayson taking back the Nightwing identity; and Bruce using Damian as his Robin, despite an earlier pronouncement to the contrary). Perhaps the other Batman titles are navigating an altogether different course -- the Court of Owls is sufficiently similar to the Black Glove, how could they have coexisted without warring or merging? But Morrison's never had much coordination with the other writers on the bat-titles, and even if Inc is shunted to a tertiary position while Scott Snyder and others take the higher-profile titles, it appears that Morrison's tale continues on, with no sharp delineations from the time it began in Batman #655 over six years ago. To be sure, his plans have evolved along the way, considerably, but Morrison loops the story backwards with flashbacks to the John Mayhew plot, and his rendition of the night Bruce rang a bell to summon Alfred almost as seamlessly as though it had all been planned in advance.
We've known since February 2012's Leviathan Strikes that the villain of this extended story is Talia after Morrison's two previous long maxi-arcs (running in three different titles) both centered around Doctor Hurt.
Once we dispense with the confusion of reboots and how it fits with Snyder, et al's work, the story remains tangled in time. Batman, at the very end of time in Return of Bruce Wayne #6, saw backwards to the vastly earlier time (the mid 21st century, it may be safe to say) when Talia's putative plan played out, a look back first mentioned in The Return when Bruce says he has to protect his allies from "what's coming, what I saw." Apparently, we see that vision (or a slightly more detailed version of it than Batman himself saw) in Inc Vol. 2 #5. It is a vision which Bruce believes will not come to pass (and given its level of horror, we may be sure will not come to pass), which puts into play that the future is malleable: Bruce was at the end of time looking back, but for reasons contained within Morrison's story (and not, likely, within Flashpoint, which was driven by other forces), Bruce believes he can alter it, but not completely. It is also clear that his vision was not complete (in Inc Vol. 1 #1, he calls it "a glimpse of the big picture", and he was despite that glimpse surprised to learn that Talia is Leviathan). He also calls the upcoming struggle with Talia "the fight of my life." And as he says in Vol. 1 #6, "Something big, something bad is coming. And no. Not everyone is going to survive it." So while he believes some portion of the vision can be addressed, he believes that some deadly portion of it cannot.
After extensive foreshadowing that the death of Damian is at stake, we receive a vision of a future in which Damian is Batman, which has featured in three full stories: Batman #666, Batman #700, and Inc Vol. 2 #5. Add in a non-incidental similarity to a reference in Batman #665 when Bruce awakens from a stupor to imagine a grinning Damian telling him that the third Batman is the worst of them all, and remembers a previous dream in which a Batman "sold his soul to the Devil and destroyed Gotham." At the time that served as an elaboration on his first foggy meeting with Michael Lane (the third "Replacement Batman" trained by Doctor Hurt). It also seemed possibly prophetic in Batman and Robin #15, when Doctor Hurt tried to deal for Damian's soul. And it very obviously hearkened to a scenario seen in Batman #666, when Lane and Damian fought a showdown using devilishly-provided longevity. I've previously written up that issue here.
The story in Batman #700 seemed to tell a story (tied in with three others in that issue) of the real future with Damian as Batman, one less haunted by apocalyptic overtones, and no indication that Damian had gained longevity by dealing with the Devil. And yet, it has a striking similarity to Inc Vol. 2 #5 in a baby who is infected with Joker virus. In that telling, Damian obviously does have such powers (rising again after being mowed down by machine gun) and the panel showing him mourning the death of Batman (apparently Bruce, but again see my earlier write-up) indicates that we are back in the #666 timeline, one which was never assured to happen, but which shows what might. Morrison didn't plan this far ahead in 2007, but here we are, and that timeline with the ultimate grim outcome – the total destruction of Gotham suggested back in #665 – coming to play, with Doctor Hurt, as good as the Devil himself, standing by the shoulder of the President, whispering bad confidences to destroy what was once his home city when centuries earlier he was the 1760's Thomas Wayne. This seems to validate that Doctor Hurt remains in the wings for future use, living until he's freed from the coffin near Wayne Manor.
Now, the story in the present takes a strange turn. Damian is cast out from Bruce's shelter, seemingly left to a high risk of death without such protection. We still have a flash forward teaser from Inc Vol. 1 #1 showing Bruce, looking over graves, seeming to quit his Batman identity before being arrested by Commissioner Gordon. With Inc. agents set up around the world, it seems as though the fight of Bruce's life is to begin, and with Damian's death perhaps the tragic end of a story being written so far with the prophetic power of Greek tragedy.