Slightly dark humor:
With the seal having been torn off and replaced, and also with the Kyuubi's chakra being torn from her, she's pinned down.
But Naruto didn't take her will.
As the seal is weakened with time, the Kyuubi manages to slip her will into one of Naruto's shadow clones.
However, lacking access to her vast stores of Chakra, about the most the Kyuubi can do is annoy him. But, it makes Naruto less likely to use his favorite Jutsu, because he can never tell when the fox will manage to slip some of it's will into one of his clones.
Eventually, the physical manifestation of Hate (the opposite side of love) obsesses over making Naruto's life miserable. The purpose is to try and get Naruto to try and release the seal or at least relinquish her chakra. All efforts fail, but as people quarrel more they get even closer. Unfortunately, things get a bit out of hand, and Naruto and the Kyuubi end up taking a roll in the hay.
The end of the story; the Kyuubi can never come out from behind the seal, but an increasing amount of affection develops between the two due to Naruto's Naruto-ness – i.e. he makes everyone love him, or at least accept him.
The ways in which the Kyuubi annoys Naruto – impersonations of him that create scenes or cause him to look stupid/perverted;
Messing with his love life;
Interfering with fights and causing him to get hurt
From within her prison the Kyuubi, the nine-tailed demon fox of legend, seethed. She was most powerful chakra construct since the primordial ten-tailed beast, the Jyuubi, and yet she was powerless before these hairless monkeys that had managed to imprison her within yet another one of their frail and pathetic mortal bodies.
The Kyuubi had no memory of the defeat of the Jyuubi by the Sage of the Six Paths; however, like all things, the Kyuubi had ancestral memories of the time before the Juubi's chakra was divided. How the pathetic monkeys had managed to manipulate the beasts into an unending cycle of destruction and confinement was still a mystery, but, being the strongest of the bijuu, the Kyuubi retained more the Jyuubi's original will and intelligence than the rest of the tailed beasts.
That formidable intelligence was dedicated now to engineering her release. The Kyuubi vowed this would be her last imprisonment. Even though she was a timeless being, ever since that damnable Mangekyo Sharingan and Uchiha clan had appeared her freedom had been constrained. She'd reigned undisputed as the most destructive force in the world, only to be controlled by a hairless monkey gifted with a fraction of the Jyuubi's powers. Madara had first controlled her to fight the Senju clan, leading to her imprisonment. She'd enjoyed a brief period of freedom when Madara had broken the seal on Kushina Uzumaki years ago to destroy Konoha, but the fourth Hokage of Konoha, Namikaze Minato, had sacrificed himself to seal the demon inside his own son, Naruto Uzumaki.
She would not give up her own existence to resurrect the Jyuubi, nor would she allow the vessel she was imprisoned in to die until she'd found some way to have that damnable seal put in place by the Fourth Hokage removed. She was a being of infinite patience, fearsome intelligence, and cunning wit. With the demise of the Uzumaki clan, the knowledge of the seal that kept her imprisoned had vanished with the deaths of the Fourth Hokage, the Third Hokage, and Jiraiya the Toad Sage.
The Uchiha clan only had two survivors now. That clan was soon to end; even Madara would eventually succumb to time. She was not so constrained. She was separated from her chakra and had lost the easiest means to influence her host. But she wasn't powerless. When her host started experimenting with shadow clones to speed up the learning process, she'd implement a stratagem that ultimately could lead to her freedom.
Sealed as she was, her power was as a grain of sand in comparison to the mountain at her disposal before. Delicacy was called for in this situation, though, as brute force was likely to bring the whole thing crashing down on her head. But subtlety and stealth, like a brown recluse on under the quilt at bedtime, would produce more results than reckless behavior. An insect bite left untreated could infect a leg and turn it gangrenous if it wasn't noticed. A small tendril of pure malice leaked out through the bars of her prison, hovering above the dank water that was ever present in Naruto's mindscape. It coalesced to resemble a candle flame, but before it could dissipate, the Kyuubi brought the entirety of her will to bear upon it. It wavered, hesitated, but didn't lose form. It flickered there, sputtering and guttering as it burning above the water, pushed about by an unseen and unfelt breeze.
The Kyuubi grinned wickedly.
It was little more than her desires given form. It's reactions would be sluggish, and once released, it would be beyond her control. But it was a start.
Naruto was training. The water level in the sewers swelled rapidly as vast quantities of chakra was used to summon a horde of shadow clones. The flame of her intentions was swept up in the flood. A few moments later, a memory returned to her the shadow clone, possessed by her desires, was subdued by the mokuton wielding Yamoto.
The glimpse of the outside world was heartening. She formed another flame outside the bars of her prison, waiting for the next surge of chakra. Deprived of her unlimited power, the Kyuubi was left with only patience. Patience and persistence would triumph where brute force had not.
The assault on the seal began, unnoticed by her jailor.
XXX
Naruto kicked back on the grass in the pre-dawn light, idly scratching at his belly as he watched the clouds above drift lazily by. There were quite a number of benefits of having unfettered access to the virtually limitless chakra of the Kyuubi, the nine-tailed demon fox, sealed inside his stomach.
The amount of energy at his disposal was ridiculous, even by his own standards. Between the chakra from the Kyuubi, his own supply, and that he had access to from communing with nature, he would never needed to work on his chakra supply. Instead, he'd trained like mad to work on his control and ninjutsu, since supply would never be an issue. Creating thousands of shadow clones at once barely left him winded anymore. His stamina, already freakish before coming back from Lighting, was now approaching frightening levels. Forcing the Kyuubi into giving up its chakra had been a bigger power boost than he'd imagined.
One of the benefits was that he could take some time to watch clouds. He no longer really needed to sleep – the amount of chakra circulating through his system now acted like a huge cup of coffee. He was wide awake at pretty much all hours now, and even when he tried to sleep he could only do so for a few hours at a time before he woke up completely refreshed.
Frankly, Naruto was bored. Since coming back from the Land of Lightning, things were pretty quiet. His search for news of either the Akatsuki or Sasuke had been useless, as so far he'd found neither hide nor hair of the organization. He'd been filling that time up with missions, seeing friends, and generally trying to figure out what the Akatsuki and Madara were up to next. But that left him with a lot of free time, and given his previous experiences fighting members of the Akatsuki, he filled that time with training.
He'd woken up well before the sun. None of the stores were open yet, and he didn't really have a valid excuse for bugging the Hokage this early in the morning. Instead, he had decided to take a page out of Shikamaru's book and find a place to relax. Laying on top of the Hokage monument and watching clouds while scratching his belly wasn't a bad way to spend half an hour waiting for the world around him to face the day.
He scratched his belly again and frowned slightly. It had been itching pretty much non-stop since the whole ordeal with the Kyuubi back in Lightning. Oh well. Naruto gave the mental equivalent of a shrug and decided to see if Tsunade had some sort of cream she could give him to help keep the itching at bay. Cheered by the thought that he now had a valid reason to bug the Hokage, Naruto leapt up from the ground and sauntered in the direction of the Hokage's tower.
That damnable seal!
Even though she pinned in place by the shrine gates Naruto had summoned when he ripped away her chakra away, she could still act. Though she couldn't even vent her frustration by lashing her tails against the bars as she had done before, her anger and malevolence was too great to be contained within her body. It was a physical entity, and even as it simmered and circulated through her body, small quantities leaked out and dissipated into the air surrounding her.
The Kyuubi growled. She focused her will, concentrating the small quantities of her chakra that were leaking into the air into a single, tenuous physical manifestation of her malice, sadism, and hate. It resembled nothing more than a thin line of fog. It wasn't much, but it at least gave her some way of interacting with her prison. The seal had been changed to something she couldn't recognize after her latest encounter with her jailor. She also had no way of properly examining the seal for structural weakness from behind her prison. The best she could do was to continue to probe blindly at the seal and hope for some sort of reaction. So far, she'd accomplished little but refining her control over the ability to manipulate the physical manifestation of her will. She called it a new tail, but it was a pale comparison to one of the real appendages. It was all she had to work with, though, so she made due.
She pulled her new tail away from the seal, a bit frustrated with her lack of progress. Beyond her prison, the streams of chakra moved rapidly as her host channeled huge amounts of chakra repeatedly. She had no idea what he was doing, but he seemed to be profligate with the use of the stuff since gaining control of her supply. Frustrated, she lashed out with her anger and slapped the surface of the stream with her hate, watching as it dispersed uselessly in the water, too dilute to convey any of her intentions.
She tried again, thrusting some of her intent into the stream of chakra to watch it his and bubble away, returning to a tranquil state almost immediately after she withdrew her new 'tail.' Watching the taint in the chakra be swept away gave her an idea. A diffuse amount of intent was no good against the torrent of chakra. But what about a super condensed pearl of loathing?
She concentrated as hard as she could, gathering as much of her intent as she could before her and compressed it into a ball. It sprung into shape, loosely formed and vaguely transparent. It wouldn't work, but this was only for proof of concept. Gingerly, she dropped the ball of hate into the flowing stream of chakra.
It hissed and danced across the surface like a water drop on a hot piece of iron, and just as rapidly dissipated before it could be dragged down the stream and turn into something useful. The Kyuubi still watched it with interest, though. She returned to her examinations of the seal, but the image of the small ball of intentions, skittering across the surface of the chakra, remained with her even so.
xxxx
"That cream you gave me cleared that itching right up!" Naruto dodged the thrown ashtray and the thrown sake bottle, but unfortunately both of those were simply decoys. The paperweight caught him right on the forehead and sent him crashing to the ground.
Tsunade smiled. "Glad to hear it. So, are you ready for your next mission?"
Naruto popped back up immediately. "Finally! It only took you a couple of months!"
Tsunade glared at the hyperactive blond and lifted a glass threateningly. Naruto quailed slightly, but nevertheless still looked immensely relieved to have something to do again. "Alright, brat. Listen up. The mission's right up your alley. It's not combat, but it is immensely important. Got it?"
Naruto wrinkled his nose. "Not combat? Man, that sucks!"
"Well, get used to it. With the destruction of Konoha, all our food stores got demolished. We need to replenish them fast before the winter, and Konoha can't afford the manpower necessary to escort the caravans in with the grain."
Naruto nodded, seriously this time. "And if we can't get grain in…"
"People starve." Tsunade picked up a piece of paper and handed it to him. "We're vulnerable right now, and the other elemental nations know this. Why fight a war if you can just kill everyone off through starvation?"
Naruto grimaced and read the mission read out. "Seriously? You want me to do this? I haven't done a B ranked mission in years."
Tsunade sighed. "Yeah, but this mission is tailored made for you. Go to Wave. Pick up forty tons of grain, and escort it back under armed guard. With your bunshin, you can do this one by yourself, free up the other ninja and merchants to do equally important work. Even if I pay you ten times the going rate for this mission, you'll still be saving Konoha butt loads of money in the long run."
Even though it wasn't quite what he was expecting, Naruto accepted after haggling a bit over the pay. He didn't really care how much he got paid, but he had to put on a show for the Hokage's sake. He quickly packed his bags and headed to Wave. He had a delivery to make.
xxxx
Even though it was physiologically impossible for a metaphysical manifestation of hatred and malice to sweat, the Kyuubi felt as though she should be drenched in perspiration as she concentrated on condensing every ounce of her intention on the rapidly spinning ball of negativity that hovered before her eyes.
She'd stopped probing at the seal. It would be close to impossible for her to make any modifications to the seal without Naruto's cooperation. She'd come so close to freedom during the fight with Pein, but the chakra of Minato Namikazi had broken through to her vessel and prevented him from tearing the seal asunder and setting her free. While she couldn't affect the seal from within her prison, maybe she could modify it from without?
The question had driven her to find some manner to affect the world outside of her prison. The only instrument she had available to her was her will, and separated from her chakra, it was a weak tool indeed. She'd been able to hijack Naruto's clones before with just her chakra. However, those clones had been worse than useless as they were little more than mindless beasts, easily subdued by Yamato during training.
But she was confident she'd found a way. This was something else. She poured every ounce of her will into her construct, focusing intently on making sure her intellect carried over. She would have a chance to test it soon.
xxx
Naruto was glad to see Wave again. The trip from Konoha was much faster now as an adult. He'd forgotten to account for his increased speed, and had arrived as the sun was setting, leaving him with extra time to kill as his contact wasn't expecting him till the next morning. He spent the time wandering around the village, taking in the sights. The bridge was just as impressive as he remembered it, and since the weather was sunny and the air mist free, he was able to take in the rather impressive vista from the bridge that he'd missed last time.
The scenery wasn't the only nice thing he noticed. The despair and hopelessness that had been ever present before under Gato's thumb was gone, replaced with a sense of optimism and energy from the people. Even though it was sundown, the streets were packed with crowds milling about, engaged in commerce, conversation, and life. Where people had shuffled listlessly in the streets, they now moved with a sense of purpose. People who refused to meet the eyes of strangers were now smiling in the streets and holding their heads up proudly.
The formerly ramshackle houses had been given a bit of tender loving care; fresh paint and construction was apparent everywhere as he strolled down main street. Fruit and vegetable vendors had a wide variety of wares for sale and the prices were competitive with what he'd seen elsewhere on his way in.
Seeing how much things had improved in the intervening years made his heart swell to bursting with joy. Inari had grown from a little shrimp into a teen; Tazuna looked younger than he had the first time Naruto had seen him. With the Great Naruto Bridge complete and the economy on the upswing, the absence of stress had smoothed some of the deeper wrinkles that lined the old man's face.
The evening was spent with Tazuna's family. Tsunami cooked a fantastic meal, and Tazuna plied Naruto with a great deal of liquor while said ninja regaled Inari with tales of his exploits and derring-do. It was a great time, and by the time Naruto stumbled off to bed, his head was spinning so much that he didn't even notice his stomach itching.
xxx
The Kyuubi felt the surge of chakra coming before it reached her cage. Carefully placing her construct in the way of the flow, she watched with anticipation as it was swept away in the flood intact.
She grinned.
xxx
The clone with the Kyuubi's consciousness blinked, and looked around. She recognized the bridge named after her jailor, but the line of wagons bearing bulging sacks was new to her. It had worked! She was so giddy at the prospect of having unfettered access to the outside world that she failed to pay attention to the fact that there were droves of clones scurrying around her.
"What are you waiting for, dummy? Get to work!"
She turned to see another Naruto clone busily tying down a cart behind her. The motion caused her to stumble though, as she wasn't used to balancing in this form. Thankfully, she stumbled into the cart she was standing by clumsily reached for the wagon bed to stabilize herself. Watching the other clone surreptitiously from the corner of her eye, she began mimicking the motions, though the process was more difficult than she thought as she wasn't used to this body, and wasn't used to operating fingers.
In addition to not having control over this body, her senses were dulled. Her hearing sounded as if she were underwater, though that was made up for by the vivid colors her eyes detected. Cursing as she fumbled the rope yet again, she wondered how these miserable creatures had ever managed to dominate her with such frail and useless appendages.
The clone that yelled at her frowned. "What the matter with you?"
Rather than respond, she simply concentrated on learning how to control her new form. With a "tsk," the other clone pushed her out of the way and tied the rope down in a practiced manner before turning back to its own cart.
The trip back to Konoha was thankfully long and boring. The long part helped, as there was plenty of time to learn how to first walk, then run, jump, and otherwise do physical activities as she struggled to learn to control her new form. The boring helped with her cover, as she didn't look out of place as she tried random activities. Given Naruto's short attention span when not occupied with a task, the other clones were engaged in similar activities to relieve their boredom.
The three day long walk back to Konoha gave her ample time to get used to the new form. That's when she started to catalog the handicaps. She had a pitiful amount of chakra at her disposal, given that she only had the clone's reserves at her disposal. Second, being a clone got her no closer to the seal, as the seal didn't carry across
The Fourth's seal had already broken once, and even now its integrity was questionable. It gave her hope. Even prisons of the hardest stone and the toughest steel couldn't stand up to the gentle and unyielding persistence of water. Like water, she would continue to probe the seal for any weakness, exploiting the gaps she found and creating enough space for her to eventually break free. Until her freedom was assured, however, the brat would live.