This is a sidestory to Ten Thousand Failings of Haruno Sakura. Or perhaps a partner story would be a better way to put it. This story takes place in the same universe and will follow Naruto on his training trip and after. Originally I just planned to have Naruto reappear at some point in the main story (or actually appear since he's never shown up in person despite being mentioned in every chapter so far) but eventually I decided it would be inappropriate. After all, the whole universe has his name stamped on it and the entire plot of shippuden revolves around Naruto. Any other character you can omit from a fanfic or write them out believably in a few lines. But Naruto has to be there in some fashion, and I decided to use this story to let us follow him for a bit to see why he is so different when he reappears.
If you don't want to read 10,000 failings of Haruno Sakura: Don't worry, just remember this story is AU, some of the world history has changed. This story takes place after the original Naruto Anime, just before the start of the filler arc. The team assignments, mission to Wave, chunin exam, invasion, Tsunade appointment to Hokage, and Sasuke retrieval arc happened almost exactly as in canon. However anything that happens in Shippuden or before either series may be drastically different.
Ten Thousand Failings of Uzumaki Naruto: Chapter 01 Lost Enroute
"An empty mind is like unto a freshly turned sod; if not sown with the seeds of love, duty and honor, the insidious weeds of treason will take root." -unknown
Jiraiya of the Sannin is a man of many parts. He is a ninja of legend, an idealist, a hermit, a self proclaimed sage, a pervert, an author, a spectacular sorcerer, a master spy, a general, an orphan raiser, a traveler, the list was almost endless. His greatest weakness was actually as a teacher. Over his life Jiraiya has, so far, trained 7 students.
His first three students were a group of orphans from the Country of Rain. He'd trained them to about genin level, given them a heavy dose of his philosophies on life, and left them. He hadn't seen any of them since the 2nd Shinobi War and had no idea if they were dead or alive.
His second group of students was his official Konoha team. Uchiha Mikoto took almost eight years to make chunin and her skills never really rose above mediocre. Only a massive amount of backroom politics by the Uchiha Clan got her promoted to special jonin just before she retired to become a housewife. Haruno Kizashi embraced Jiraiya's idealism and many of his teacher's philosophies but spent virtually his entire career as a genin. Namikaze Minato graduated top of his class and would have excelled under any teacher. He actually taught Jiraiya more techniques than he learned.
It wasn't really intentional; it's just that Jiraiya preferred a hands off teaching style. While he enjoyed lecturing students on his ideals and teaching them ninjitsu techniques, he vastly preferred letting students grow on their own to find their own skills and their own solutions to problems.
His most recent student was another victim of Jiraiya's unique teaching style. In fact barely 6 months into the training trip, which largely focused on basic shinobi skills and Jiraiya's philosophies, Jiraiya was ready to begin the 'do it yourself' method of his teaching style.
"Naruto, tomorrow we start the next phase of your training."
"Great! What am I going learn? The Giant Ball Rasengan? Elemental Training? One of those cool Toad Techniques?"
"Nope!" Jiraiya said with a grin. We're going to train your practical world knowledge and spy skills."
Naruto, with considerably less interest asked "How do we do that?"
"Simple, you'll travel on your own for a bit and I'll catch up with you once I've checked on a few places."
Now Naruto was a little skeptical of this plan. He'd spent most of his life alone and hadn't learned any fantastic skills by doing it. Moreover, he'd only been out of the village a handful of times and was willing to admit his geography was a little fuzzy. He wasn't even entirely sure where he was right now. Now he was willing to give wandering aimlessly on his own a try. It could be fun, probably cheaper to since Jiraiya wouldn't borrow any of his money but Naruto had one giant problem with the plan.
"How will you find me?"
Jiraiya laughed. "Won't be a problem, you couldn't hide from me if you tried."
"Hey! I totally could! I bet I can hide so good you'll never find me!"
Jiraiya laughed. Not a little laugh, but a laugh that shook his body, a laugh from way, way down deep, a wild throat ripping, maddened howling laugh. "Sure." He finally said. "You could ditch me. Now lets get some sleep, I'll be gone when you wake up."
True to his word Jiraiya was gone the next morning when Naruto woke. Jiraiya had absolute, one hundred and ten percent, unshakable confidence in his ability to find Naruto. He had every possible advantage in such a chase. He owned a continent spanning spy network (it still wasn't global but he was working on it) with agents in every major city, most large towns, several hidden villages, criminal organizations, and even a few roving agents. Naruto had no support network whatsoever. Naruto was also the most noticeable and memorable ninja ever. He was loud, he was orange, and he had bright, blaring blonde hair. He was also a creature of habit; Naruto practically lived off ramen and gravitated toward ramen stands, even if he managed to hide his tracks Jiraiya could simply go to ramen stand owners until someone remembered Naruto. Jiraiya's last big advantage was simply location. The two were currently camped in the country of Rivers, leaving Naruto with only two choices of direction.
Naruto could follow the road east, which would take him into the heart of Fire Country. Or he could follow the road south which depending on the route would either swing him back eastward and into Fire Country, or swing westward and take him into the south eastern parts of Wind Country. In Jiraiya's mind the kid would have a good adventure for a month or so, in a relatively safe area, then Jiraiya would catch him, all was well.
When Naruto woke he was actually kind of pissed off. He was a proud kid and wasn't happy with the way Jiraiya said that he had basically no chance of avoiding the toad sage. Sure Naruto had been a little annoyed and worried about Jiraiya basically abandoning him, but was currently more pissed about Jiraiya's dismal of his skills than he was about being alone. He'd been alone most of his life, he hated it, but wasn't really afraid of it. But pride goes before the fall, and the boy made a decision (that in hindsight would be one of the most important decisions of his life.) He decided Jiraiya was not going to find him. Naruto would show his teacher that nobody underestimated Uzumaki Naruto. If Jiraiya did find him, it would be because Jiraiya was just that much better, but Jiraiya was going to half to earn it.
So the first thing he did was something he'd done before every prank, something he hadn't really done since he was put on team 7. He sat down and started planning. Naruto was not a smart kid. Honestly he was kind of dumb. He had a certain animalistic cunning and was a fantastic improviser. What he sucked at was storing information, organizing it, and drawing useful conclusions from facts he knew. Part of the problem was his rather limited academic knowledge (partly his instructors fault, partly his own). He usually had such a limited pool of information to work with, so why think about it?
What he was good at was thinking quickly and not worrying about what he didn't know. Instead of thinking about what he didn't know, he focused intently on what he did. He didn't know where he was. Not a problem. He didn't know how long he'd been gone from Konoha or even what day it was. Not a problem. He had no clue where the road went in either direction. Not a problem.
What Naruto did know was simple; he knew that Jiraiya knew where the roads went. He also knew how to avoid people looking for him. Ideally you went somewhere the other person didn't know, where you knew all the hiding spots. Or if you couldn't do that, you tried to go where neither of you knew the place, so at least it was even. So, Naruto's plan was basically to go off road. He didn't know what was off the road, and he just hoped Jiraiya didn't either. Path decided, Naruto packed his gear and set off. He barely slowed down to summon Gamakichi to give him some company while he tree hopped. (If asked what direction he'd gone Naruto would have simply said "this way" or "that way" or "off the road". He had an intuitive sense of direction but no real map reading skills. Directions like east and west were largely useless to him. But if you asked Gamakichi, who was actually quite good at cartography, he'd have said they went almost perfect north.)
Ninja tended to travel not much faster than a normal person. However when they wanted to a Ninja could hit a steady 'marching' speed of about 15 miles an hour. Even a genin could usually cover between 100 and 150 miles a day without much trouble. Naruto couldn't really go faster than a standard ninja, but what he could do was hold a marching speed for a lot longer without much trouble. He could march for eighteen or twenty hours, go to sleep, wake up and do it again with no trouble. He'd decided to keep going until he hit a town of some sort. Something that took nearly three days.
Whether you call it fortune, or profoundly bad luck, largely depends on where you happen to be at the time, but Naruto was noticed the moment he crossed the border into the country. (For those of us who obsess about maps and immediately looked up River country once it was mentioned, and then pulled it up again when we discovered North, we know exactly why entering this country could be…unfortunate. For the less cartography inclined…suffice to say the Country of Rain frowns on tourism.)
The man called Leader was naturally surprised when Uzumaki Naruto stumbled into the Country of Rain, and with great excitement informed his fellow members of Akatsuki. Itachi and Kisame immediately volunteered to set out and collect him. Konan immediately vetoed them both.
"No, not after last time," she said. "He'll panic when he sees you both and fight you at every turn. This requires delicacy and subtlety, a woman's touch."
It would take Jiraiya a week to conclude his business and start looking for Naruto. He checked out south western Fire Country and couldn't find a trace. Not worried, he went to wind country. He didn't even find a whisper. Officially freaking out, he put out the word to his network that Naruto needed to be found, and he started searching like a mad man.
His toads where maddeningly unhelpful. Naruto had told Gamakichi that he was hiding from Jiraiya. By the laws of the contract they could not/would not betray a summoner in any way. Even to help a senior summoner find his apprentice. They couldn't even tell Jiraiya if Naruto was alive or not. They wouldn't even take messages.
Needless to say, it was a very nervous Jiraiaya who turned up in Konoha a full three and a half years after the training trip started. He was… hesitant to admit he'd barely trained Naruto at all before he lost him and that he'd spent three years basically on a manhunt without bothering to tell Tsunade that his apprentice was even missing. Yes, Jiriaya thought to himself, this is going to hurt really bad, as he walked through Konoha's massive gates.