Disclaimer: I don't own Naruto in any form. All characters of this story are owned by their respective owners. No copyright infringement intended. As far as Disclaimer's go, I'll only be putting this up here once. It's already obvious I don't own Naruto. If I did, I certainly wouldn't need to dedicate a fan fiction to it.

AN: Naruto's finally over. It's a little hard to believe and certainly saddening, but that's the sad truth… Doesn't mean our fandom has to die though. If anything, I think this opens new possibilities. Anyway, being a rather big fan of Naruto (it's my second favorite anime/manga. And I can't even say that for certain, considering how I still debate whether or not I love it more than Evangelion or not. So I guess it's tied for first), now that the series has finally come to an end I thought now would be the perfect time to start a new Naruto ready for quite a long tale, as this will be one of epic proportions.

Before we start, shout out to Serious Sam for being my beta for this chapter. If you aren't reading it already, you guys should totally check out their story My Precious People.

Well, without further ado, here's the first chapter of Making Up For Lost Time.

After Twelve Years…

Crying.

That's the first thing Kushina remembered; her baby, her precious little boy, crying. This wasn't the first time she'd woken up. No, she'd slipped in and out of consciousness for years, but every single time the first thing the first thing that came to mind was her baby, her little Naruto. She wasn't sure how much time had passed in the outside world, but she was certain it had been a long, long time.

She wanted to see him so badly. She wanted to hold him in her arms, talk to him, care for him, and love him like only she could. She wanted to be a mother to her son so badly – but what could she do? She'd been in a coma for what seemed like years upon end, and yet things could still get worse.

Here she was, trapped in a dark cell. The bare stone floor beneath her was cold and aside from a thin blanket, some hay in the corner of the room, and two buckets in the opposite corner there were no other 'comforts' – and she used that word very loosely. She hadn't always been here; before this she'd been in a hospital room of sorts, as her captor did not want her dying. But she'd been waking up much more frequently than before, so with her out of the woods per se, whoever was in charge had apparently decided that she be moved to somewhere less conspicuous and more…secure.

The first time she woke up, she learned that Shimura Danzo was the one holding her captive. Minato had told her of him and his secret ANBU organization, Root. She knew he was bad news, and so did her husband – they just never thought he'd do something this treasonous…

"Kushina." The red head turned. Kneeling next to her was her one and only; the only man she'd ever loved and the father of her precious child – her husband, Namikzae Minato, the Yondaime Hokage of Konohagakure. He had been in a coma with her, in and out of consciousness much like she was. They didn't always catch each other awake, but that didn't matter as neither of them remained conscious for very long.

"Yes?" she replied, her voice weak and somewhat raspy from years of little to no use. He put his hand over hers, a deep determination showing behind his blue pools.

"I'm sorry," he replied, his voice in a similar state to hers, "It's taken so long… but I finally have enough Chakra… we're getting out of here…" Danzo had kept them weak. He had made sure that they'd never gained enough Chakra to fight back and had only given them enough care to keep them barely alive. He underestimated exactly how smart Minato was though. The Yellow Flash was no one's prisoner and he was about to prove just that.

"Get ready… We're getting out of here… and then we'll be able to see Naruto again…" Minato gave a shaky smile to his wife, who returned it with one of her own.

==X==

"And that's our report, Hokage-sama," said Kakashi. Sarutobi Hiruzen, the Sandaime Hokage sighed. He wondered why nothing was ever simple when his surrogate grandson was involved – no, nothing was ever simple at all.

"I see. Thank you, Team seven is dismissed. Kakashi, could you stay behind? There are some things I would like to further discuss with you."

Nodding, Hatake Kakashi complied with the Hokage's wishes. Turning to his students, the jōnin told them they were dismissed for the day and that they should go home and rest. Sakura nodded, a relieved smile appearing on her face. Sasuke gave his usual "Hn" and Naruto merely shrugged.

Kakashi expected the responses he received from Sakura and Sasuke, but not Naruto. He'd been too… subdued. He'd been that way ever since leaving Wave. His blond student looked like he had a lot on his mind, and the copy nin wasn't sure what was wrong with the boy.

The three genin left the room, closing the door behind them. Usually, this was around the time Sakura would ask Sasuke for a date, he'd refuse, and then Sakura would be asked out by Naruto, also refusing – however, only two of the four things occurred today though. Sakura asked Sasuke out and was rejected as usual, but when she turned around expecting to have to deal with Naruto, he'd merely looked at her briefly, seemingly lost in thought over something, before offering her a goodbye and walking away.

Sakura stood there, slack jawed and wide eyed. Naruto was acting weird.

What the hell just happened? She asked herself.

==X==

Uzumaki Naruto was a brash and loud boy. He was unrefined, had almost no manners and very little care for them. He didn't mind being this way; mostly because he didn't know there was any other way to be. No one had ever taught him such things. There was no one who could – scratch that, there was no one who would. The Hokage was a busy man, he couldn't devote a large amount of time to Naruto, and everyone else aside from Teuchi and Ayame hated the boy (he was wrong, of course, but he didn't know that).

Kakashi was a mystery to him. He honestly didn't know how the man felt about him since he seemed so indifferent in general. Despite wanting to believe otherwise, he was positive Sakura didn't enjoy his company and the only thing she did was fawn over the Uchiha. Sasuke himself thought Naruto was below him. Naruto heaved a sigh.

Truth be told, he'd not been feeling too great since his mission in Wave. Sure, they'd saved the day and all that, but that was exactly why he was feeling down now. In Wave, where nobody knew him or what burden he carried, he was accepted. Hell, he was hailed as a hero but here, here in his own hometown, he couldn't walk down the street without being glared at or ignored all together. He couldn't buy anything without prices being doubled or sometimes tripled, and he couldn't go to many of the restaurants… Ramen being his favorite food isn't the only reason it's all his diet consisted of…

The contrast between the public reactions he'd received in Wave and what he received here was really getting to him and he was certainly feeling down. He wasn't sure the mask he'd created when he was younger – the one that hid his true persona could last much longer. He wasn't sure he could continue to grin and bear things – he wasn't sure he could continue being the happy knucklehead he was viewed as. He wasn't even sure he wanted to. And somewhere, in the deeper, darker parts of his heart – the parts that he couldn't fix – he wasn't sure he even wanted to remain in Konoha.

Heaving another sigh, Naruto trudged on, doing what he could to ignore the villagers around him as he made his way to his apartment. The apartment where he'd spend yet another day alone.

==X==

"So the Kyuubi's chakra has started to manifest itself?" said the Hokage, the question more rhetorical than anything. He wasn't sure he liked what he was hearing. On one hand, if Naruto could harness it correctly, the Kyuubi could be a great asset to the boy as well as the village… but on the other hand, Hiruzen knew that this could turn into a disaster.

"Yes… though, he seemed in complete control while using it, maybe a little more brutal and careless, but it was still him. Currently, Hokage-sama I'm more concerned with how he's feeling. He's been fairly reclusive since we left Wave," replied Kakashi. Any of his usual disinterest was gone. Though he acted the part most of the time, it was part of how he coped with his losses, but that didn't mean he didn't care for Naruto. He was happy to have his Sensei's son on his team, and after seeing his performance in Wave, he was determined to train his team harder. He'd almost lost his students and he was tired of losing the people important to him.

Hiruzen leaned back in his chair, inhaling from his pipe. Everything Kakashi was telling him was troubling. Naruto was unhappy? That would not do. The Kyuubi could free itself based purely on the child's mental state. Hiruzen frowned, knowing something had to be done to ensure nothing of the sort happened.

Maybe it's time I call for Jiraiya? The boy will certainly be happier if he learns of his godfather, and I'm sure my student would be happy to teach Minato's boy. It also wouldn't be too bad of an idea to have Jiraiya tell him of Kushina, thought Hiruzen, even though she had her enemies, there is little consequence if he knows of her. It would also help matters if her name unintentionally happens to slip out at some point. We've already thoroughly hidden her connection to Minato after all… Yes, this will have to do for now.

The Hokage leveled his gaze on Kakashi and said, "For now, try to bring about a friendship between him and his teammates. I will call Jiraiya and from there we…" the Hokage meant to continue, but a flash of yellow at Kakashi's back stopped him in his tracks. His eyes widened, not believing what was in front of him. Kakashi, having felt a presence turned around, and his visible eye widened much like the Sandaime's.

"S-Sensei…?"

Standing in front of him on shaky legs was the Yondaime and his wife – two people who'd been confirmed to have died the night the Kyuubi was sealed. They looked malnourished and thin, but they were certainly alive.

"We made it… I'm… So… Glad…" Minato's eyes closed and he collapsed to the floor, exhausted. Kushina, who was still capable of standing, if only barely, kneeled slowly next to her husband, worry over his condition evident in her eyes. Watching Minato fall had also shaken the Sandaime out of his shock and he immediately barked orders.

"Boar, Rabbit, seal this room! No one gets in or out unless I say otherwise! Cat, get our best medic-nins over here now. Tiger, get me Inoichi and Kakashi," the Sandaime paused here, looking the Jounin in the eyes, "Find Naruto. With everything you just told me, this couldn't have happened at a better time. I think it's time he met his parents."

==X==

Shimura Danzo was a man of few words, and even less emotion. It was rare that he let any of them show through, even anger but today – today it could not be helped. The old war hawk had underestimated his opponent and there was no way it wasn't going to come back and bite him the ass. He stared at the empty cell in fury, wondering how he could have been so careless. His frown deepened as he questioned himself, thinking over what possessed him to not find a better way to prevent Minato's actions.

Danzo sighed to himself, deciding that now was not the time to dwell over his mistakes of the past. Minato and Kushina were gone, his plans foiled, and now he would need to flee Konoha. He'd managed to avoid Hiruzen's eyes until now, but this little indiscretion would undoubtedly send the entirety of Konoha's wrath down upon him.

"Sai."

Immediately, a pale child appeared at Danzo's back, kneeling before him in a show of the utmost respect. He seemed no older than 12 and his voice sounded void, hollow of anything.

"Yes, Danzo-sama?"

"I am leaving the village, but you must stay here. Keep an eye on things, especially Uzumaki Naruto. I want reports on what happens in Konoha every so often. Make sure nothing is outdated, but don't become suspicious. That is all, you are dismissed."

And with that, Danzo walked into the shadows, intending to never set another foot in Konoha – unless it was a situation that was favorable for his ambitions…like being named Hokage.

==X==

Inoichi was led into the office where he was met with the sight of the Yondaime and his wife. His mouth dropped open and he paused, shocked beyond movement. As a ninja, and head of the Interrogation Division there wasn't much that surprised him, but when two people who were confirmed to be dead twelve years ago suddenly pop up alive in the Hokage's office, you're going to be speechless.

"Wha…?" Yamanaka Inoichi couldn't even get out a proper word.

"I shall explain later," the Hokage said as he diverted his eyes from the medic-nin healing Minato to look at Inoichi. "There's not a lot of information we have at this point, but we desperately need to know what happened. Inoichi, look through their minds and tell me what you see. Start on the day of the Kyuubi attack then work your way forward till today. And do it as quickly as possible!"

Inoichi, though still shocked knelt next to Kushina and got to work immediately. She smiled at him and nodded her head, understanding what he had to do as a medic-nin tended to her injuries. Nodding back to her, he ran through a series of hand signs before coming to a stop and staring at her.

"Seishen sanpo no jutsu!" With those words, Inoichi descended into her mind. The both of them remained motionless for nearly 15 minutes before Inoichi blinked, then blinked again before his face turned stony. He turned to the Sandaime, a deep frown of his face.

"Hokage-sama… this is very bad."

The Sandaime from frowned in response, but ordered Inoichi to speak and thus, the mind walker told everyone present exactly what he saw and how grave things were.

==X==

Minato had just used the Hiraishin to transport himself and the Kyuubi deep into the forest, far from Konoha and the villagers. The Sharingan was no longer in the Kyuubi's eyes, but the Yellow Flash highly doubted that the absence of it would suddenly make the enraged Bijuu more docile. In fact, it probably made the threat even worse as the fox now had control over itself and was far better at using its body than the masked Uchiha who had been manipulating it.

And ss much as Minato hated to admit it, he only had one option left. Briefly flashing away, he returned almost instantly with Kushina and their son.

"Kushina… we don't have much time… we have to seal the Kyuubi into Naruto."

Kushina's eyes widened. "No!" she screamed, "There has to be some other way! Our baby boy… We can't do that to him, Minato! He's our son!"

"There isn't time for anything else… and I certainly couldn't ask someone else to let their child bear this burden."

"But… But…" Kushina's eyes welled with tears before she buried her face into her husband's chest, sobbing. Minato tried to stay strong for her, but tears were rolling down his cheeks as well.

"I'm sorry, Kushina… this is the only option we have left…" Summoning an altar and placing Naruto on it, he turned to the Kyuubi as he ran through hand seals. Appearing behind him was an apparition clothed in a pure white Kimono. Its face was that of a demon – sharp teeth, piercing eyes of the darkest black that instilled fear instantly, and horns atop its head.

The Kyuubi, understanding what Minato intended to do narrowed its eyes and launched forward to attack him – only to be stopped dead in his tracks. Kushina, though disconnected from the Bijuu, still had some measure of control. Using her chakra chains, she bound the Kyuubi and prevented him from harming Minato and Naruto. Her husband looked to her, a sad smile on his face as he launched forward. Through the use of the Shiki Fujin, he pulled out half of the Kyuubi's chakra and sealed it into himself. The Kyuubi, dazed yet unrelenting continued to struggle as Minato turned to his son before speeding through another set of hand signs.

Roaring, the Kyuubi thrust its massive claws forward, taking advantage of a slip in Kushina's focus. She was tired, and so afraid of what her son would have to endure that her attention drifted for the briefest of moments. Seeing what would happen if they didn't intervene, Minato and Kushina, in a desperate attempt to rescue their child, jumped into the path of the Kyuubi's claws. A single claw tore through Kushina and Minato's bodies, stopping right before it could impale Naruto. Blood trickled down the Bijuu's claw, but Kushina and her husband did not care if they were to die so long as Naruto was safe.

"Hakke… Fuin," Minato struggled, crimson liquid bubbling over his lips and down his chin and then the seal activated, dragging the Kyuubi into it where it would find itself spending its foreseeable future. Only seconds after the Biju was sealed, the Shinigami who ruled over the Shiki Fujin prepared to take Minato's soul, but the Shinigami did not count on one thing – Kushina. The red headed, hot-tempered, wife of the Yondaime Hokage refused to let such a thing happen to her husband. She wouldn't allow the Shinigami to force Minato into combat with the Kyuubi within its belly; not after the sacrifices they'd already made. If they were going to die, she was going to make damn sure they at least got to rest in peace.

With the last of her strength, her chakra chains materialized and grabbed at Minato's soul, wrapping around it and pulling.

"Didn't think… I'd just let you take… his soul… did you, dattebane…?"

The Shinigami, seeing what a mere mortal was daring him to do, pulled back. The tug of war continued on, but Kushina's strength was quickly draining and the Shinigami would not be denied. With a vicious tug, it pulled forth Minato's soul, Kushina's chains, and by extension, her soul as well. With a swift downward strike, it severed their souls from their bodies and vanished as they dropped lifelessly to the ground – or at least, that's what the Shinigami thought. Kushina had not participated in the Shiki Fujin, and so by taking her soul as payment for his summoning – even if it was only a little bit of it – he voided his part of the contract. Though half of the Kyuubi remained sealed within Minato, neither he nor Kushina would have their souls taken from them as payment.

The life drained out of Kushina and Minato as they lie motionless in the clearing, their son crying all the while. Then, where there were once only three bodies, there were now seven.

Standing over the downed forms of the Yondaime Hokage and his wife were Danzo and three of his Root operatives. A small, sinister smile crept onto Danzo's lips. Before him was an opportunity he couldn't pass up.

==X==

"From there," said Inoichi, "Danzo's operatives rushed them to their base. He wanted to take Naruto as well, but after setting up suitable faux corpses of Minato and Kushina he could already hear you closing in. Seeing as how Naruto would not stop crying, he saw him as a flight risk and left him where he was. Once at his base, his operatives did everything within their power to tend to Minato's and Kushina's injuries to make sure they pulled through. It was touch and go, but thanks to Kushina's Uzumaki genes and Minato's new status as a Jinchuriki, they made it through. This was the point where Kushina passed out, and she stayed that way for quite a while. She woke up a year later based on a conversation she had with Danzo. She'd been in a coma and he told her that the minute she and Minato were out of the woods and awake he would begin turning them into his perfect weapons. After that, the two of them were conscious very infrequently over the next twelve years. This is the first time they've managed to stay awake for very long."

The Hokage was furious, his fists clenched around his pipe and within seconds, it snapped in half. He had been lenient with his old teammate, he'd tried to get him to shut down Root without having to resort to violence, but now the man had gone too far. Sarutobi Hiruzen would have Danzo's head; he swore his very life on it.

"Find Danzo," he said, looking to the ANBU who'd brought him Inoichi. "Take any reinforcements you think you need and once you locate him, alert me immediately. Danzo has severely overstepped his boundaries, and by the end of this day I will end his life. Go!"

The Anbu complied immediately. In Konoha, there was one thing that was absolute – no one crosses the Hokage.

Well, there it is. The first chapter's done. I hope to hear from you guys in the reviews. I'd like to hear your opinions and any constructive criticism you may have to help me improve. Hopefully the next chapter is up around this time next week.

Translations:

Hakke Fuin: Eight Trigrams Seal

Hiraishin (no jutsu): Flying Thunder God jutsu

Jinchuriki: Power of Human Sacrifice

Shiki Fujin: Reaper Death Seal

Seishen sanpo no jutsu: Mind walk jutsu