Disclaimer: I'm pretty sure I haven't transformed into Kishimoto Masashi overnight, which means that I don't own Naruto or any of its characters.
Warning: As usual, some manga spoilers.
Secret Paths
The eyes of a doujutsu user can see many things.
The Sharingan can see the formation and movement of chakra that make up a jutsu, and instantly pierce through any illusion.
The Byakugan can see through solid objects, and even detect the chakra pathways in a human body.
The Rinnegan can see...well, no one really knows the full extent of what the Rinnegan can see. But it's certain that it can see far more than normal eyes.
In most cases, the ability of a doujutsu user to see things that others can't is an advantage. In battle, it's an asset that can make all the difference between life and death.
But some of the things doujutsu users can see are things they might prefer not to.
There are rumors, whispered into the ears of younger siblings by older ones, that doujutsu users can see ghosts. Most people imagine that this means they can see spectral figures of shinobi who've died in battle, with gory wounds still marring their bodies.
This may or may not be true. But either way, it's so much more than that, because the most enduring ghosts are not of people, but of places.
There isn't a shinobi village on the continent that hasn't been invaded at least once. Wars have wracked the ninja countries since time immemorial, since even before there were ninja. Over and over, the ninja villages have been destroyed and rebuilt. If one were to dig under any of the Hidden Villages, one would find layers of wreckage beneath them, testaments to homes, shops, and schools obliterated by past conflicts.
For those whose eyes can see more than the norm, those old, wrecked places still exist.
Neji learned this early, having activated his Byakugan at a younger age than any previous member of his clan. It was the anniversary of his father's death, and he was wandering aimlessly through the streets of Konoha, stewing in his anger at the Main House. He wasn't really paying attention to where he was going, so at first he wasn't surprised when he ended up getting lost. As he looked around, trying to orient himself, he noticed strange things about the buildings that surrounded him. The architecture was in an archaic style, one that hadn't been popular in over fifty years. The trouble was, very few buildings that old had survived the Kyuubi's attack-most of them had collapsed when the Demon Fox's rampage made the ground shake and its monstrous chakra rippled through the air like sound waves made visible. An isolated few had survived, like the Clan Head's home in the Hyuuga compound and the Nakano Temple in the Uchiha district, but a whole street full of them?
The next thing Neji realized was that this peculiar little street was utterly silent. He heard no footsteps, no voices, not even the swish of displaced air as a ninja ran across the rooftops above him. No lights gleamed in the windows of the houses that lined the street.
Very slowly, Neji turned around and walked back the way he had come. When he reached a familiar street, he breathed a sigh of relief, although he couldn't have said why.
After a few similar experiences, he mentioned the phenomenon to an older cousin, who explained that his eyes were capable of seeing the remnants of places that no longer existed. Neji wasn't sure how to feel about this: it was a relief to know that the strange thing that had happened to him had an explanation, but there was also something eerie about the idea that the village was full of silent, empty places where no living soul walked.
Now that he was aware of the existence of such places, Neji was able to avoid entering them. He did so out of some vague fear of who (or what) he might encounter on those deserted streets.
Uchiha Sasuke, on the other hand, had no one to explain the "ghost places" to him, but between his natural intelligence and the Sharingan's ability to see the purely spiritual chakra that composed them, he was able to eventually figure it out on his own. Unlike Neji, he made a habit of exploring the streets and plazas that no one else could see.
Neji feared meeting the dead in those phantasmal landscapes, while Sasuke hoped for it.
Nagato realized what his eyes were showing him in a different way. He became aware of the unnatural nature of Rain's own ghostly places by noticing that they were the only parts of the village where it never rained. He would be walking down one street in the middle of a torrential downpour, turn a corner, and suddenly find himself in a cobblestone-paved alley that was dry as a bone. Once, while fleeing from a group of thugs as a child, he turned into one of the dry streets and watched his pursuers thunder right past the entryway, not even giving it a second glance. Because, of course, they couldn't see it at all.
For Nagato, these locations were not places of fear, as they were for Neji. Nor were they places of hope, as they were for Sasuke. For him, they were places of refuge. They were places where the sky itself didn't cry for the fate of the land beneath it, places where there were no sounds of battle, places where the air didn't stink of decay. He sought the dry streets whenever he needed to escape, whenever the weight of his pain became too much for him to bear.
It was in one such place that he pierced Yahiko's flesh with black metal and resurrected him as the first and greatest body of Pain.
The eyes of doujutsu users see things that most others cannot. They see the streets and homes and places of business that have fallen to the wars that plague the world. The places that only they can perceive are forever growing in number, and there are always new paths for them to discover.
They all hope that it will not always be so. Neji hopes that when his youngest cousin Hanabi grows up, she won't see new streets appearing month after month and year after year.
Sasuke hopes that one day, when a little boy with Sakura's green eyes and his brother's name plays hooky from Iruka's classes, he will eventually discover that he's explored all the "strange roads" that exist in Konoha, and that there are no more emerging.
Konan (who has heard the stories of these places from Nagato) places one hand on her rounded belly and hopes that her child's eyes will see the dry streets far outnumbered by the rain-soaked ones.
And the ironic thing is, they all know that the one who will make these wishes come true is a boy who has never seen those places at all.
A/N: This is another one of those stories that I have no idea what part of my brain it came from. Regardless, I hope you enjoy it.