A/N (It's a bit of an essay before the update, sorry about this, but it has to be said.)


So first up thanks for all reviewing so much! This story has nearly exceeded my previous story despite being only half as long and a pretty different beast! 276 reviews is more than I dreamed of, and this story isn't really even half way through.

There's a but.

Judging from the last chapter, more than a few of you don't like the Naruto/Baka thing that is going on in this story. Guest declared this chapter had ruined the story, InARealPickle (please turn PM back on so I can answer your review properly) and Arthain (cool name) didn't like how disconnected Naruto was from things. I think there are a few more people out there with similar thought, so for everyone in that boat, I implore you give me but a few minutes to give a bit more insight into the whys of Baka and Naruto.

Let's start with a bit of background. Cause and Effect. For an effect, there should be a cause. Unexplained plot devices or sudden Deus Ex Machina are, to my mind, a bit rubbish. Thus when something happens in my story it happens with a reason for it as best I can do. I'm not perfect at this, but I try.

So when I write the story, I use the canon as the original flow of the universe. If nothing influences the flow, it won't change from the canon. Neji is still a jerk, Hinata is shy as hell, and Kakashi reads his orange book. Team 7 goes to Wave, an invasion happens and Hiruzen dies. If it happens like canon I probably won't write about it.

So when Naruto is removed the flow is changed. Gaara dies. Haku, Zabuza and Gato die differently, and Neji remains an arrogant son of a bitch. It's like dropping a stone into a still pond and watching the waves.

But moving Naruto out of Team 7 is a change, and you have a variety of options if you remove Naruto from team 7.

The first and most used is just to shuffle things around. Usually one of Kiba or Lee get bumped to team 7 so Naruto can do whatever in the other teams. That's alright as a basic fix, but removing Naruto from the entire academy makes this invalid.

Option 2 is to bring someone into Naruto's space. Commonly Sai can be used (although how he is dead last amazes me) or another character who wears a red shirt and is killed quickly. I expect many people thought Baka was going to die in the Wave so Naruto rejoins Team 7. Nope.

So in comes the OC, but does this change things? Hell yes. If he's a whiny unlikeable idiot who makes Sakura look athletic then it changes everything. Sakura, Sasuke, Hinata and Kakashi are the main ones affected in general by loss of friend, rival, love interest and "child" in that order.

So I didn't want that. I wanted to disrupt the flow as little as possible. Then I saw the opportunity for Baka. Let's look at him in a bit more detail.

He very much is like Naruto. In fact, he ends up in the same situation a lot of the time. But he's different. He's not hated by the village, instead drawing inspiration from an inferiority complex that stems from his rivalry with Sasuke. His signature technique, my version of the Spirit Transformation Technique, brings out his inner strength like an inverse Susannoo, strengthened by his indomitable will and weakened when he feels scared. He's a confidence fighter, much like Naruto. His personality is like Naruto's, so Hinata draws the same strength from him.

Now, people seem to dislike the fact I had Jiraiya take him to get back Tsunade and had Naruto declare him his apprentice. Let's examine the few sentences where I touch on this again:

'

"I will consider it. You have taken Baka as an apprentice already though."

"How?"

"It is your right as a Sannin, and he was with you when you came in with the new Hokage."

Jiraiya shrugged his great shoulders.

"Very observant. He helped bring Tsunade round to the idea of coming back, and fought well. His Spirit Transformation Technique is remarkable. Tsunade really saw Dan in him; it was his technique as well."

'

Let's examine it in detail. Does Jiraiya directly confirm that Baka is the apprentice? He does not. He notes Naruto's observation that he noticed Baka instead of being wowed by Tsunade, Jiraiya and a bunch of ANBU. Remember, Baka isn't hated, he'd be more than likely ignored.

Now, what is interesting is that Jiraiya is willing to dump Baka out of his care to take on Naruto. Canon Jiraiya would never do that, and would never consider dropping Naruto for anyone else. Baka is not Naruto.

So why would Jiraiya care? Simple, he used Baka as a tool to get Tsunade back. He doesn't care hugely about the boy, although he makes a good substitute for Naruto. Baka is like Minato, only he isn't. Naruto is the Godson, not Baka. Naruto is the Junchuuriki, not Baka.

Remember cause and effect. Without Naruto and his learning the rasengan, Tsunade has no reason to come back. Cause and Effect. Baka, looking like Nawaki and using Dan's jutsu is the perfect foil for Naruto in this situation. We don't see the arc because Naruto does not. (and everyone is sick to death of the bloody thing)

So now we've sorted out why Jiraiya would take him as the apprentice, let's sort out how Baka is like canon Naruto, and how he is not.

Physically he's different. By personality, both are pretty much the same. But we don't know a huge amount about Baka because Naruto doesn't show the required interest to learn it. What are Baka's hobbies? What does he do with his time off?

It's all too easy to just assume that because he acts like Naruto he is Naruto, and so it seems a lot of people have determined he eats ramen by the bucketful and raises flowers (both canon hobbies). The thing is we just do not know enough about him to assume he is Naruto.

Simply put, we don't actually know that much about Baka. We don't even know his name.

As a side note, he can say Dattebayo because it is a word. It's a word. Anyone can say any word. Believe it. Just because someone else says it famously doesn't mean other people can't. And that's the bottom line, cos Onmysignalunleasewords says so. I refuse to believe that saying Datte- is a genetically passed down tic only available to the Uzumaki clan, so I changed it. Don't like it? I got two words for ya. (you know what they are if you get the reference)

...

So to get back on track with this, there is a good reason I made Baka how he was. I could have crafted another character who was unique and useful for the story in his place, so I'll agree at a casual glance that it looks like a "cop-out" as Guest put it in their review. But I don't want to develop a character for that purpose because this is a story about how a different Naruto becomes more human. I could have given him a name, a backstory and had him have some heart to heart conversations that made Naruto human in a few chapters. But that would have been the easier route.

Instead, I chose to choose an option that didn't disrupt the canon flow. I wanted someone to fill his place a little different to Naruto but similar enough to keep Sasuke, Sakura, Kakashi, Hinata and everyone else he touches on the right track for as long as I need them to be on the canon path.

When he's done that, you know exactly what going to happen. Much like Jiraiya and every evil villain, once a tool has run its course...

So I hope you understand why Baka is Baka, why Baka is Naruto and more importantly why Baka is not Naruto. If you want to discuss this please let's do it by PM and not review (reviews should be for the story and not me explaining the story) and I hope this helps.

The stone was dropped into the pond at the start, and the ripples keep going outwards. Although at first the effect is small, it grows every second and gets bigger and bigger. Then the change affects everyone. Cause and Effect.

Onwards to the story...and a meeting with Tsunade.


Tsunade spun round in the chair, hand steepled as the ANBU squad walked into her office. The woman standing beside her behind the desk sighed deeply.

Tsunade was currently feeling the rush of power that came with becoming Hokage, and had been greeting every single person that entered her office the same way, by spinning in the chair like she was a supervillain welcoming a nemesis. Shizune swore she'd heard mutterings about wanting a trapdoor installed. Tsunade had almost considered commandeering a cat for the day, before realising what the only one available was.

"Talon, Pig, Hare. Welcome to my office."

"Hokage-sama, welcome back to Konoha."

Talon greeted his new boss with a smile, not that it was visible.

"Now I remember that voice. You grew up well."

"You remember that? I was six at the time!"

"I remember it. I'm a good doctor. How's your shin?"

She smiled as she knew Talon was a probably blushing a little under the mask. The mood was relaxed. It was entirely unbefitting of a military tyrant meeting her head of elite operations, but hey, new leader, new ways right?

"The ANBU await your command lady Hokage. We welcome your leadership."

"Good. I've seen the reports of your work and I'm happy. I have no doubt that you will continue as usual."

"Of course Lady Hokage. We await your commands. We will spring into action!"

The man's excessive motion as he spoke the last phrase caused Tsunade to shake her head gently.

"The Old Man did mention you were eccentric."

"Did he mention witty, handsome and brilliant as well?"

"One of those, I'll let you choose which one."

She knew he was smiling behind the mask.

"Eyes off my apprentice though."

He staggered back, his gaze snapping away from Shizune.

"How?"

"I just know. Treat her wrong and I will take you apart at the seams, sow you together again and then punish you further. Clear?"

"Hai."

Shizune sighed. Was the ANBU captain handsome under the mask? Ah well, she wasn't interested. Being a doctor was her life, and add in being Tsunade's apprentice and keeper...well it took its toll on personal life. She never got a chance.

Tsunade was about to begin anew when a crossbow bolt arced gently through the window and landed on the floor, bouncing off the wood.

She barely blinked as she kept her gaze locked on Talon, who was staring at it like it was about to explode.

"Care to explain how someone fired a crossbow through my window Mr. Big Shot Captain?"

"That wasn't fired. That was thrown. And I think I have someone you should meet."

"Get them in here before I drag them in for throwing a crossbow bolt into my office."

Talon disappeared out of the window and stayed out for a couple of minutes. He then reappeared in the place of one of the cushions that had once been on a Sofa. He cursed as he headed back to of the window.

Pig sighed and handed a wad of cash over to Hare.

"He's learned new tricks it seems."

"Seems so."

Talon gave an exasperated sigh, and left the window again. There was a thump, the sound of metal on metal, then silence.

Talon and Naruto then came in through the window.

"I win again Lion. Nice trick with the sword though, I owe the Hokage a cushion."

He held up the gutted rag that had a sword hole in it and tossed it into a bin. Tsunade leant forwards in her chair.

"Talon, who is this? Why are you fighting them? And get me that cushion as soon as possible. Double stuffed, duck feather. The cover should be in red or blue. First mission for you, D-rank. Got it?"

Talon's head drooped. He thought he'd been done with that rank.

"This is Naruto...I'll leave you to talk to him."

The name rang a bell in her mind as the ANBU trooped out. A character from Jiraiya's first book, from before he had begun to write terrible smut. She remembered the years before, when Dan had been around. When she had believed in love. She'd found the book amusing, like reading the work of a nine-year old. Minato had liked it though, always the nice boy.

But who names their child Naruto? She cast an eye at the section of bookcase she knew slid away to reveal the black files that Hokage's kept of the most important secrets.

She stood, and smashed the bookcase cover off the wall. She reached in and picked up the pile of dusty folders. Time to start doing things her way. She checked the one at the top, ignoring the sound of confusion from Shizune.

"So Naruto, let's see who and what you are."

She read the first few sentences of the file and stopped.

She looked at him, still hooded and cloaked, staring straight at her with his single visible eye. Not much of his face was visible.

"Take down your hood."

He did. His short hair was a little matted and dirty from the time between washes, and his face was streaked with small amounts of dirt. But she could see it. She could definitely see it.

She read a few more lines.

"Stomach."

He lifted it up, she observed, and then she nodded. The shirt went back down.

She read the rest of the report and put the file back down beside the pile of other folders.

"I'll memorise the rest and burn them later Shizune. I don't like the dark secrets; I will not govern from the shadows."

Shizune smiled. It was good to see her master governing as she always did, bluntly and without any backstabbing. She was a direct person, in thought, word and deed.

She turned her full focus on Naruto.

"Name. ID. Rank."

"Uzumaki Naruto, 002953, Unranked."

"Good. First order of business, you are now a chunin. I'd offer you a flak jacket but I doubt you'd want one. Specialisations and techniques."

"Stealth and Assassination, expert in crossbow use, proficient in the use of blowgun, wire, kunai, tanto, poisons and genjutsu."

"Kill Shizune in the next ten seconds."

"What?"

Shizune barely had time to think before she found herself viewing, as if floating above her body, the sight of Naruto slicing her head off with a blade. She broke the genjutsu and ducked as the sword blade actually came to fulfil the vision.

She swung out a leg, but Naruto was flipping away, firing a blowgun at her. The dart caught her shoulder and she pulled it out before throwing senbon needles at him. He caught them with his cloak as he spun, then brought the crossbow up.

"Stop."

He stopped, and stowed the bow on his back. Shizune ran a hand over the point where the blowgun dart had hit and began to drain a little of the blood, muttering about a weak toxin.

"Go outside, strip, and declare your love of flowers, kittens and all things soft and cuddly. It will benefit Konoha."

There was a pause before he began to move for the windows.

"Stop. I know enough about you now."

He had stopped in mid air, grabbing the window ledge, and swinging himself back in.

"You're more hardwired to obey orders than anyone I've ever seen. The reports of your actions are confusing but make sense when you think about them from the right mindset."

"My mindset?"

"Probably. I probably have grounds medically to have you sectioned. I doubt you'd be in there too long though, you'd probably escape."

She sighed.

"What do I do with you? Throw you into ANBU, where Talon will appreciate you more? Give you free reign to follow missions? What do you want to do?"

"Your orders Hokage-sama."

She stared him down.

"Want to do. Not programmed to do."

"Missions."

"What kind?"

"Any you order me to."

She span round in the chair and threw her hands up in exasperation.

"Kami I think I need a Yamanaka to examine you just to see how your brain works. That would be a bad idea given your training and other conditions. Which reminds me, Shizune could you summon Danzo for me?"

"Of course Tsunade-sama."

She hurried out.

Tsunade just stared at Naruto, who found himself simply returning the gaze, looking into her eyes. Mostly. Much like with Anko, there was another, more round view within sight. He tried to ignore the roundness.

"What. To do. With you."

"I just desire to do missions. It's my purpose in life to kill and help Konoha."

"Interesting. So, when you kill someone, you are sure that killing them will help Konoha?"

He did pause for a small moment.

"If they are orders, I must assume that my superiors have reason to do so, and if I do so without orders, it has been during battle or with appraisal to killing the target."

"How many kills have you made on people who just got in the way of your target?"

"Five."

"Name them all."

"Three guards who didn't see me coming, one who did, and one other."

That 'other' was definitely something more. Her gaze narrowed a bit, catching his eyes.

"Who was the other?"

"A maid."

"What happened?"

He tried to remain focused but his memory was firing back into its perfect technicolour life again. He tried to block out the screaming.

"She...the screaming."

"What?"

"She found me by accident and screamed, so I had to silence her."

Her eyes widened a little. That sounded more like Root pragmatism, but it didn't sound like him from the rest of the interview. That was interesting.

"Did you not think to knock her unconscious?"

"Had to stop the screaming."

"It's ok, you can stop remembering now."

He shut down his brain as fast as possible with Hinata's face and its conflicting emotions. It was more soothing.

"You are very odd. You are a cold hearted killer who would kill my assistant, who is like a daughter to me, at the slightest word, yet loses control when you hear screaming. It's in Anko's reports on you. You knew she made them right?"

"It seems logical for her to do so for the Hokage, yes."

"Good. You're not an idiot. And you're not a psychopath. In fact, you're more normal than you think. Glance at my chest again for more than a second and I promise you I will cave your face in."

He tried not to break eye contact.

"Still don't know what to do with you. I'm worried about what happens if you get bored. Goodness know what would happen if some lucky girl screamed in joy with her young man and you came in through the window all kill on instinct. You know what I'm talking about right?"

"No."

That had her surprised, then she realised she shouldn't have been.

"You've never had the talk have you?"

"The talk? Is it something Konoha shinobi are required to have?"

"Well yes. And no. It's about how babies are made."

"Oh. Sexual reproduction. I know of it."

Tsunade prayed he wasn't going to be that practical.

"So when I say the girl is screaming in pleasure?"

"A side effect of the copulation process?"

She sighed. Of course, he was all about the practical.

"If, and I say if, someday you ever enter the process yourself, you may understand."

"I am not yet at an age where reproduction would be beneficial, puberty has only just begun to happen."

She laughed. He was for real. He was verifiably both the most sheltered and open person in the world because he had no shame, no social stigma. Just spoke his mind, unrelentingly. But there was emotion in there somewhere. It had been glimpsed.

Shizune bustled back into the room.

"Danzo is outside waiting for you Tsunade-sama."

"Good. Naruto, hide somewhere in the room, I'll close my eyes and count to two."

Two seconds later she opened her eyes and he was gone. She decided to read the small number of black files on her desk. They made for slightly odd reading, but the information was committed to memory.

She summoned up her best authoritative tone.

"Enter."

Danzo walked slowly into the room. It just wasn't the same when it wasn't Hiruzen. Talks like this, assuming they happened, should be in the dark, in the shadows, late, when nobody would see. He felt almost exposed in the light.

He chided himself for such nostalgic thoughts. He would do what was necessary for Konoha in memory of his friend and rival.

"Tsunade-sama, May I be one of many to congratulate you for returning in our hour of need to fill the mantle of Hokage. Hiruzen would have been proud of you."

"I'm sure. I take you know this is all business Danzo."

"Good to hear you are a woman of action."

"Right, I've taken a look at Hiruzen's black files. You come up. As does this...Root?"

"Yes. A discrete team of highly trained shinobi capable of carrying out less savoury missions for the good of Konoha. We were officially disbanded at the end of the last great war, when the Fourth was appointed Hokage."

"Ah yes, your methods are?"

He evaded the obvious verbal trap.

"Were Lady Tsunade, the organisation has been disbanded. The methods were rigorous, testing, demanding. They form the toughest of shinobi to perform the toughest of missions where hesitation could cost hundreds of lives."

"By which you mean inhumane, bordering on torture, and that they are emotionless killers."

"Such were the sacrifices that needed to be made for the good of Konoha."

That sounded like Root pragmatism and sounded like everything she stood against as a medic.

"No more. Disband Root immediately. Properly. Fully. Do not keep a private army from the world. Release to me a full roster of Root shinobi, so I can place them into ANBU positions or where they are needed. No more dealing in the shadows. This is a new age Danzo. No more secrets. No more darkness."

"But the usefulness of Root is..."

"Expended. Exhausted. Konoha is weak, but I will rebuild it stronger than ever. We will become the greatest of the nations, moreso than ever before. Do not mistake my approach in the light for weakness Danzo."

Danzo sighed. It was as he had feared.

"Naruto, come out again."

A small, potted plant in the corner transformed into Naruto.

"Danzo-sama."

Danzo gestured to Naruto, who stood to attention, hood raised and cloak hanging around him.

"Lady-Tsunade, I present Root. Naruto has been my sole operative for some years now. Hiruzen entrusted him to me when he was small when the orphanages stopped accepting him. Now he is, as you must agree, a fine shinobi."

"He is. But he is all your Root force?"

"Times were good for Konoha before the invasion, the number of missions that needed doing were relatively low, and so I needed only one operative."

"Is this the truth Naruto?"

"Yes."

The answer escaped him before he could prevent it. He realised that he couldn't have resisted anyway.

He blanked on his Byakugan and saw the light behind Danzo's bandaged eye. The technique was strong, but it was being used on him? Surely he should have targeting Tsunade to keep Root intact.

"I give you my Root shinobi, much as I entrusted him to Hiruzen. Do well with him Hokage-sama."

"And yourself Danzo?"

"I would wish to be part of your senior advisors and elders to offer council as you might require it."

"I would welcome such council."

It was logical, but Naruto saw a different path. There was an old military saying he had found during his studies with Root about keepings one's enemies closer. He suspected that both parties were using the ploy to keep the other in check.

The symbiosis was stunning. He realised that over the years Danzo and the old Hokage must have known each other perfectly.

"You are dismissed Danzo, I will seek your council when it is required."

"Thank you Lady Tsunade. Good luck Naruto, may you continue to serve the leaf."

"Hai Danzo-sama."


Danzo left the room and walked sedately out of the tower, using his stick in an obvious manner. The illusion of frailty was important to keep himself safe in Konoha. Still, he had only a small window before Tsunade had him followed.

He ducked into an alleyway and took off towards one of the numerous passages under the walls that he had installed. The Root had been cut from the leaves, but it would continue to serve. Even without Hiruzen controlling it, it would continue. Even if it and he faced censure.

The Root would continue to grow.