Disclaimer: I don't own Naruto or any of its characters.
Missing
It takes Konoha a long time to recover from Pain's invasion. Yes, he resurrected all the people who were killed, but the buildings are still destroyed, houses and shops and municipal offices smashed into tiny fragments of stone and wood. Water pipes and electrical cables were demolished, so what's left of the streets are flooded with puddles that no one dares to touch because they might be electrified.
Despite this, they do recover. Everyone throws themselves into the work of rebuilding, and upon the formation of the Shinobi Alliance, other nations send workers to help. Tazuna and Inari even come all the way from the Wave Country. Doton and mokuton ninjutsu accelerate the process, and little by little, the beauty of Konoha is restored.
One of the most time-consuming, and heartbreaking, parts of the process is sifting through the rubble for any possessions that might still be intact. Although they're grateful just to be alive, the village's citizens can't help feeling their eyes well up with tears when they discover that a photo album with pictures of a deceased friend, or an heirloom that's been in their family for generations, has been irreperably damaged. And they're equally joyful when they find that a child's beloved teddy bear or an old Ninja Academy graduation certificate has somehow miraculously survived.
The most macabre task falls to those responsible for searching the location that used to be Konoha's cemetery. Identifying the scattered unearthed bodies, making new coffins and headstones, and reinterring them once the debris has been cleared, reminds all those doing it of how much the village has lost over the decades of its existence.
What the shinobi assigned to this duty find puzzling, however, is that some corpses are unaccounted for. Sometimes all they find is an empty, broken coffin, with no matching body to be found anywhere in the wreckage.
They assume that the missing bodies-particularly the old ones, which can't be much more than fragile skeletons by now-were simply disintegrated by the Chou Shinra Tensei blast. They console the families, who've now lost one more thing on top of everything else. Priests say prayers for the souls of the missing dead, exhorting them to rest peacefully despite the mysterious disappearance of their earthly remains.
But sometimes, on moonless nights when the wind whistles across the top of the crater that was the old Konoha, those who were assigned to graveyard duty wonder.
Some of the bodies that disappeared were old enough to have simply been disintegrated. But not all can be explained away so easily. What about Gekkou Hayate, who died just before Orochimaru's invasion? What about old Uchiha Kagami, who was killed with a poison that, as a side effect, should have preserved his body perfectly? What about Ebisu's grandmother, the owner of a grocery store who died of a heart attack barely a week before the destruction of Konoha? What about a dozen others whose deaths were too recent for so much decay to have occurred, or those who were killed with jutsu that prevented such decay entirely? Why are their corpses among the missing too?
At times like this, they remember the Gedo Rinne Tensei. The surreal thing that appeared in the center of their village, opened its mouth, and spat forth the souls of those who had been killed that day. The glowing masses of chakra that, for the first time, were visible outside the constraints of the bodies they resided in. The way the souls floated across the village, streaking purposefully towards their bodies. The way dead friends, family, and comrades, began to breathe again.
They remember that Nagato had been exhausted when he used the Gedo Rinne Tensei. It had taken the last of his strength, and they all recall how hard it is to control a jutsu when one is in such a depleted state. They wonder, too, how he had selected the proper souls from all the ones milling around in the afterlife. He didn't even know the names of most of the people he killed, so how could he possibly have specified who to bring back? Or had he even specified at all? Maybe he had just opened the doorway, and anyone who wished to could go through it.
Late at night, when they can't sleep, they wonder about this. They think about the missing bodies, and the gateway between worlds that Nagato wrenched open. They slip out of bed, push aside the curtains, and gaze out the window over the darkened landscape. They find their eyes drifting over the sloped surfaces of the crater, drawn to the neat white rows of stones behind the temple that's been rebuilt in the northwestern quadrant. They pretend that, even from this distance, they can pick out those stones that stand guard over empty coffins.
And they wonder.
A/N: As I've probably mentioned in reference to a couple of my other fics, I've always loved ghost stories, so naturally I get the urge to write one every once in a while. (Although I suppose technically this is more of a zombie story...)
Here's another fun thought: With so many souls coming back all at once, what's the guarantee that the right ones made it into the right bodies?