Hey guys, I have a couple of mutually exclusive theories:
It's a no brainer really, we know he has her body and is up to something. She will one way or another return back to life.
Another implied thing is that humans have souls, and once a soul it's gone it cannot be brought back. BUT that's not what we see actually. What if the real deal was the neurons, and that surge of magic coming out of her so to speak was actually the veil at the Departement of Misteries obtaining an imperfect copy of someone's consciousness? What if that veil is just a failed try by the atlantians, Merlin, or whoeevr at, say, the magical version mind uploading? Like when people simulate neuronal networks on their computers and think "just if I had a map of the synapses in a brain I could simulate it". Right, you may get something resembling consciousness. But it wouldn't capture the subtleties of the millions of chemical reactions ocurring in a particular neuron. Like people resurrected with the stone, or proffessor Binns. People who cannot learn new things, who really don not function as normal human beings.
Harry said something like "magic in hpmor works intent-based". BUT what if that's limited by whoever programmed "intent" in magic? Say, the atlantians. It can do just as well as they could at their time. Maybe they roughly understood how the brain works, but didn't understand enough of the neuron's internal mechanism. Maybe whoever programmed "reparo" built in certain things in it, like a complete enough feature set for everyday's work, but left things out that were algorithmically too complex, like fixing cloth. Maybe the creator of the resurrection stone/veil set (the vail stores the data, the stone let's you get it back) didn't know how neurons exactly worked, and couln't simulate them properly with magic or make the neurons alive again. I think the atlanians had science, and maybe that's exactly why they perished, and that's the reason they could program so many spells, they knew the algorithms.
What if the universe is just a lisp-like interpreter, and runs the earth as software? Someone discovered how to execute an eval from within, and everything is data, so they just self-modified the code to include different functions which are activated when someone with a particular genetic code says some random words with the "intents" of the wizard as parameters. But their sciece wasn't that advanced actually. The muggle world could have discovered magic a while ago if it wasn't for that genetic lock which someone along the way put to monopolize magic. And that's where Harry comes in. He has the algorithms (or can write them with his scientific knowledge), and he can mess with the source code. And that's what Quirrel is trying to stop (I don't know why though). He doesn't want Harry to know about spell creating, and Mcgonagal doesn't realize why he advises her not to let Harry have access to that, she thinks it's just because they are being "responsible adults" and children just are not meant to have access to that.
Mayby souls actually do exist, and when you use the resurrection stone you are actually bringing back the spirit, but as it doesn't have a body anymore it cannot function in this realm of reality. So he will get her spirit back, fix her body in the usual scientific ways (see above) and join the two with the elder's wand.
He brings her back somehow (duh) but I still don't know how.
He is going to surprise us all and take a dramatic deathist approach. Actually Dumbledore is right, Hermione now just belongs to another realm and is gone forever from this world. Harry's attempts end up in failure, or he actually somehow brings her back but she is in zombie-mode and wants to go back to heaven, just as Rowling wold have liked (very unlikely given the author of the fic).
EDIT: Thanks, I thought line braks would be kept, but it seems like I need an extra new line every paragraph.