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What Remains?

Summary:

Naruto wakes up wounded, alone, and unable to remember anything beyond his own name.

As he struggles to piece together who he is, he's pulled into a conspiracy that reaches all the way to the top of Konoha. Meanwhile, friends and enemies alike are searching for him, and he's not sure how to tell the difference.

When he's lost everything that makes him Naruto, he must discover what remains.

Notes:

(See the end of the work for notes.)

Chapter 1: Only a Name

Chapter Text

A roaring ball of fire rushing towards him. The shrill scrape of a kunai dragging against his bones. The crack of his fist against someone’s jaw.

He gasped in pain as his legs collapsed beneath him, his good arm barely softening the impact of the landing. He closed his eyes and rolled over, but his bones ached for him to stay still.

The chirping of birds. Black sparks of electricity. Someone calling out a name he couldn’t remember

He roared and forced himself back up onto his knees, and then on his feet. Naruto? His brain supplied. His legs wobbled beneath him, but he clenched his teeth and kept walking. He was stronger than that. Right?

“Naruto. Your name is Naruto,” he muttered. His head pounded. It only got worse every time he tried to recall the details of how he got here, where his wounds had come from, or who the black haired boy was that called out to him.

A pair of red eyes staring down at him. Some whispered words he couldn’t understand. The fade to black as he fell unconscious.

Another wave of agony washed over him, and it took everything he had to keep his consciousness from sinking in the flood of memories that followed. He went down to his knees, then hunched over and slammed his fist into the dirt. And did it again. And again and again and again. He kept going until his knuckles were bleeding and the newly exposed roots in the ground were a red pulp. Tears fell from his face and he didn’t resist the racking sobs that overwhelmed him.

He fell to his side, curling his knees to his chest despite the ache in his joints, and cried. “Naruto. Your name is Naruto.” He repeated it until he drifted into merciful unconsciousness.

***

Kakashi ignored the sting of the branches as he darted through the trees. He ignored the weight of his drenched clothes making every jump more difficult. He ignored the voice in his head screaming at him for being slow and useless again. He’d gotten quite good at ignoring things in his lifetime.

“Kakashi…”

But Pakkun didn’t need to say anything. He’d felt that dark chakra too. He wasn’t sure if it was the curse mark or the Nine Tails; it could be either or both. Kakashi pushed harder, splitting the branch beneath him with a loud crack. The whole forest shook, but he didn’t dare stop. Especially not as the monstrous energy receded and the only noise left in the forest was his own violent rush through the trees.

When he did stop, it was too late.

They were gone; Naruto and Sasuke both. The only proof they were ever here was the littering of weapons throughout the valley, and the dark ash the rain hadn’t managed to wash away yet. He took in the scarred landscape surrounding him. The impacts of jutsu - or perhaps their bodies - had created dozens of small craters in the rock face of the cliff.

“Pakkun?”

The tracking dog was whisper-quiet when he spoke. “Their scents are gone, Kakashi. I’m sorry.”

Of course. He should have known this would happen. He must have forgotten who he was; Kakashi wasn’t supposed to have a family.

His hands balled into fists at his side. The rain was cold against his face as he looked into the sky, nails cutting into his palms. Blood trickled down onto the ground, mixing with the rainwater and washing away. When he was younger, he had convinced himself loss would get easier with experience. A rotten lie that was.

They’re not dead, Kakashi. He took a deep breath and unclenched his fists. The grief would have him later, but if there was any hope for his team he needed to act now. Orochimaru wouldn’t have killed them. They were too useful.

“Come on Pakkun. We’re going home.”

“But what about Naruto and Sasuke? You’re not gonna look for them?”

“If they’re far enough away that you can’t catch either scent, the search radius is already too big. I think Orochimaru has taken them both. We’ll go back to Konoha, report to Lady Tsunade, and then make a plan to find them.”

Kakashi turned to leave, not waiting for an answer, when the glint of metal at the edge of the valley caught his eye. It was a Konoha headband - no, two of them. He picked them up, and noticed a scratch across Sasuke’s. He put it away, stared at Naruto’s a moment longer, and then took off his own.

He pulled the ends of Naruto’s headband tight around his head, covering his eye once more. He would save Naruto and Sasuke, and Orochimaru would pay. No matter what.

***

“What do you mean they’re both gone?”

Kakashi swallowed back a bitter reply as the hokage stood and slammed her first into the desk. Wood splinters went flying well past his face. There was an overflowing stew of rage and grief in her eyes, mirroring his own. Jiraiya stood to the side in what Kakashi presumed was a rather solemn silence.

When faced with too many emotions to display at once, Kakashi defaulted to his usual mask of professionalism as polished as it was shallow.

“It is as I said, Lady Tsunade. Pakkun and I arrived at the Valley of the End, where I suspect Naruto and Sasuke clashed. By the time we got there, they were gone, with no useful tracks to follow after them. I believe the two fought to a standstill, and Orochimaru recovered both of them.” He had to make an effort to keep his voice straight, to keep the venom out of his words when he said that traitor’s name. He didn’t need to clarify why Orochimaru might have wanted to collect Naruto; none of them doubted the bastard would love to get his hands on a Jinchuriki.

“We can’t eliminate the possibility that it was the Akatsuki that got to him,” Jiraiya spoke up. “They’ve worked with Orochimaru in the past, and the extent of their abilities and resources is unknown. They could have even worked around Orochimaru and taken both Naruto and Sasuke for themselves.”

“Speculation,” Tsunade barked back. “It’s possible, but we don’t have time to consider every possibility when we don’t have any concrete intel. Like Kakashi said, the best lead we have right now is Orochimaru. Jiraiya, I want you in pursuit of it immediately.”

“No, Lady Hokage,” Kakashi got out before Jiraiya had a chance to respond. “With all due respect, they were my students. I will not stand idly by and wait for news of their recovery - or worse.” He let the words hang before continuing. “I will be out there, finding them.”

Tsunade’s brows furrowed and her lips pursed as she placed both hands on the splintered desk, leaning forward ever so slightly. Her eyes were locked onto his, and he could practically feel the anger burning within her. “You had your chance to find them, Kakashi, and you failed. Jiraiya is the best spymaster Konoha has; if anyone will be able to get word on their location, it will be him. He knows Orochimaru, how he thinks, how he works. He is the best shot we have to get Naruto and Sasuke back.”

Kakashi took a step forward, gaze just as fixed onto her. “Jiraiya has failed time and time again to put Orochimaru down. Regardless of his claimed intent, he has demonstrated an inability to deal with him properly. I assure you, Lady Tsunade, I will have no such hesitations.” This time, he did not put any effort into restraining his anger.

Jiraiya went to speak, but was silenced with a wave of Tsunade’s hand. The staring contest that had begun between her and Kakashi continued for another several breaths before Tsunade relented, taking her hands off the table and bringing one up to massage her forehead while she spoke. “Fine, Kakashi. You and Jiraiya will go together. You will bring Naruto and Sasuke back. And so help me god, if you fail or get yourselves killed, I’ll bring you back to kill you myself. Am I clear?” Kakashi and Jiraiya both nodded their confirmation at once.

“Good. You’re both dismissed. I want you outside the village within the hour.” Kakashi turned to leave, mentally readying himself to deliver the news to Sakura, when Tsunade spoke up once more. “Oh, and Kakashi. If you ever speak to your hokage like that again, it will be your funeral.”

Kakashi faced her again, eyes closed and crinkled to imply a smile that definitely didn’t exist under his mask. “Of course, Lady Tsunade.”

***

Kakashi stood outside the door of the Haruno residence, still not ready to say the words that needed to be said. Delivering the report to Tsunade was a challenge, but Sakura was something else entirely. His students - whether they admitted it or not - placed their trust in him. Sakura had placed her trust in him. And he broke it.

Now he’d break her heart.

He had debated not telling her. Jiraiya hadn’t even thought to. If he had kept his mouth shut, they could've been halfway to Oto by now. But as much as it would be easier, he knew not telling her would only cause more pain later.

Jiraiya cleared his throat from a couple paces behind him, and Kakashi sighed. He raised his hand and knocked on the door, once, twice-

The door flung open, with Sakura just behind it. She was sweaty, her lip was bleeding, and there was a bruise around her left wrist in just the shape of her right hand. What stood out the most, though, was the hope in her eyes. It stung.

“Kakashi? Are Naruto and Sasuke alright? They must be at the hospital. I can head over-”

“Actually, Sakura,” he said, “I think we should sit down.” He nodded his head towards the hallway she was blocking.

Her face paled, and all the hope she had vanished. “No, I don’t want to sit down. Where are Naruto and Sasuke?” She persisted.

“They… We don’t know, Sakura. Their last confirmed location is in the Valley of the End. We suspect Sasuke made it to Orochimaru and brought Naruto with him.”

There was a heavy silence before Sakura spoke again, voice laced with a brittle certainty. “Okay, so what? We just need to find Orochimaru and get them back. You’re the renowned Copy Ninja Kakashi, and he’s Jiraiya of the Legendary Sannin,” she said, gesturing her hand out in Jiraiya’s direction. “Can’t we just go get them?”

Kakashi winced at the desperation in her words, and placed a hand on her shoulder. “Sakura… It’s not that simple. I know you know it’s not that simple. Orochimaru is powerful, and has all kinds of tricks up his sleeve we don’t fully understand. It would be-”

“I don’t care,” she spits out as she takes a step back. “I don’t care. I don’t want to hear it either. What are you even trying to tell me Kakashi? That we’re just letting them go? You’re too afraid to go rescue your missing students? The village’s last Uchiha and- and whatever it is that Naruto is?”

If Kakashi winced earlier, he all but crumpled now. His tongue was lead in his jaw. “No Sakura. That’s not what I’m saying. I’m saying you’re not coming.”

Sakura was stunned. He saw it on her face while her eyes flicked from him to Jiraiya and back until they eventually settled on the older of the two. Tears were pooling in her eyes. “Oh. Of course. I should’ve known. Nobody wants weakling Sakura along as dead weight.” She shoves Kakashi aside, marching towards Jiraiya.

“Fine, then. Leave me behind. But I refuse - refuse - to be cast aside like this again.” She was shouting now, jabbing her finger into Jiraiya’s chest for emphasis. “Give me the summoning contract for the toads.”

What?

Kakashi wasn’t sure where Sakura was going when she started yelling, but he certainly wouldn’t have guessed that’s where it ended.

“What?” Jiraiya asked

“Give me the summoning contract for the toads.” Her back was to Kakashi as she spoke, but he knew the stubborn look of defiance she could wear and he had no trouble imagining it on her face now. “If you don’t believe I’m strong enough for this, I’ll need to prove there’s nothing that Sasuke or Naruto can do that I can’t. So I’ll summon giant toads and breathe fire if that’s what it takes.”

She whirled back around to face Kakashi and moved until she was splitting the distance between him and Jiraiya. Tears ran down her face, but her words stay composed. “I’m sick and tired of everyone treating me like a joke, but I’m especially tired of them being right. I’m tired of being saved by everyone around me and not being able to return the favor. I’m tired of being left behind. So give me the damn contract.”

Jiraiya continued to stare at her in silence for a couple of seconds before he nodded dumbly. “Fine, fine. You know, normally I wouldn’t be so flippant with something as serious as this, but…” He stared at her as he pulled out a tiny scroll from his pocket, which expanded in size with an injection of his chakra.

“Well, if nothing else, I suppose I owe ‘ya.” He concludes the thought as he unfurls the large scroll, revealing blank paper under the most recent signature: Naruto Uzumaki.

“Now, first thing’s first, you’re gonna need a little blood…”

***

Pain. That was Naruto’s first memory. A throbbing pain that coursed through every fiber of his being. Before he saw or heard anything, before he smelled the earthy aroma of dirt and root vegetables, before he tasted blood on his lips, before everything else, there was pain.

He was lying down. Naked, save for the bandages wrapped around his abdomen, and arms, and legs, and… well, everywhere, really. A thin sheet of cloth failed to smooth out the scratchy mound of straw he was laying on top of, and another served as a blanket.

Once it was clear he wouldn’t fall asleep again, Naruto opened his eyes. Two clusters of candles on opposite sides of the room offered just enough light to see. Now he understood the earthy scent he’d been smelling; he was literally underground. Clay, dirt and stone were molded into a dome shaped room without any windows or entrances or exits, excepting a single archway into a larger, unlit space.

The room was sparse, but Naruto was grateful for it. The less time spent analyzing the space, the more he could spend on remembering what exactly had happened. His breath quickened as he struggled to recall anything past collapsing in the forest.

“Naruto. Your name is Naruto Uzumaki,” he said with a smile. It was a small victory, but it was also a good start. He roused from his horizontal position, using both arms to push his torso upward. They ached, but it was his abdomen that rebelled against the maneuver, cramping and quivering enough to almost make him fall halfway through. But he felt too stiff in the bed, so he grit his teeth and pushed through.

“You are… a Ninja? Yeah, probably. Who else gets…” He looked down at his bandages, taking a moment to run his hand over the biggest looking injuries and wincing at the pain in the center of his torso. “Stabbed through the chest? Ouch.” A part of him was glad he didn’t remember that bit.

He slid his legs over the raised bed of straw, abdomen screaming at him even louder for the twisting motion, but he did his best to ignore it. “Okay Naruto. You are from… ” The answer never came. There was a weird grey fog obscuring a blurry image of what seemed like a village, but that was all.

He eased forward, adding more and more weight to his legs until he was standing on them fully. They trembled, each step a small torture, but they held. For now, that was enough.

He walked along the edge of the circular room. He ran his right hand along the walls, feeling for any imperfection and finding none. “Okay, fine, scrap that. Your name is Naruto Uzumaki, and you became a Ninja because…” he drew out the last syllable, letting it hang in the hair, but again there was only a fogginess and concepts of memories he reached for but never grasped.

“Damnit. Damnit damnit damnit.” He stopped, pulled his hand away from the wall, and rubbed his face with both hands. “Why can’t you remember anything, you stupid moron? You didn’t just show up in the middle of the woods, half-dead and alone. What’d you do, hit your fucking head too hard?” He growled out the words, but as his frustration ebbed he considered them more thoroughly. Maybe he did hit his head too hard. Okay. Someone’s obviously found me and is taking care of me… maybe they can heal me?

With a new line of thought, Naruto changes his focus. Brute-forcing his head to call forth memories obviously wasn’t working, so the best thing he could do was figure out where he currently is and who was caring for him. He grabs one of the candles off its stand and carries it through the hallway.

The rest of the house, as he had decided to call it, wasn’t quite as spartan as his room, but he also wouldn’t call it “well decorated” either. The hallway led into a wider room that was primary living space, kitchen, study, and dojo all at once. There was one wooden tatami table with space for four to sit at, and a futon that worked as both couch and bed. A cast iron stove for cooking. A small set of cabinets to hold the various supplies for it. There were a couple of potted plants throughout the space, but he wasn’t sure how they grew without any direct sunlight. The only thing that stood out in its ornateness were the bookshelves, each containing dozens of books: histories, economics, chakra theory, medicine. Whoever lived here had a little bit of it all. The thought of reading them filled him with a sense of dread, but they might at least fill the gaps - the large gaps - in his memory.

As he finished his surface-level inspection of the place and prepared to dig through cabinets and trunks, he heard the rumbling sound of stone grinding against stone, and light began to filter into the space from over his shoulder.

He whirled around, looking upward to a rectangular section of stone that seemed to just melt away. As more open space appeared, he had to shield his eyes from the bright light that invaded the otherwise very dim space. There was a silhouette of somebody standing just outside. The stone that had melted suddenly started forming together, creating an even staircase for the man to enter through.

Naruto dashed to the side, trying - failing - to find something substantial to hide behind. The logical part of him knew this was likely the man that had found and cared for him since he fell in the woods, but the primal part couldn’t ignore the reality that this man was a stranger that had him cornered. Evidently, he was too slow, because the man walked down the stairs with a jubilant expression on his face and looked straight towards where Naruto had fled. He was a tall man, well built and rugged looking, with a mop of egg-white hair. He wore a plain brown shirt and black cargo pants with bulging pockets; Naruto couldn’t tell what they were full of, though. Most notable of all, however, were his eyes - or lack thereof, he supposed. Each eye was shut, but the lids were recessed on his face, as if there were no eyeballs at all underneath.

Before he had a chance to react, the man was speaking. “Naruto! You’re finally awake. I’m sure you must have many questions, but I’ll start with an introduction. My name is Shibito.”

Notes:

1. I've aged up the Konoha 12 and all their cohort, from 12 to 16 at the start of canon. This is just because I didn't want to write teenagers that young, and you wouldn't want to read me writing teenagers that young.

2. I'll be keeping the characterizations of the characters relatively the same as Canon, but you can expect minor differences here or there, especially with Kakashi or Sakura.

3. Shibito is not an OC, not really anyway. They are a canon character in disguise. Have fun guessing if you want!

4. I'd like to offer a massive thanks to Dakeyras, Mehraea, and the general r/NarutoFanFiction Discord. Their feedback and discussion regarding this work was invaluable.

Thanks for reading my fic, hope you enjoyed.