AN/Synopsis: I suggest that you read this before reading the main story since it will help you to understand my train of thought since this fic took some serious thought to put together. I noticed a pretty big inconsistency within the Naruto timeline. The inconsistency involves the Ame orphans and their age in relation to Naruto's parents' ages. In the anime and manga we are at least led to believe that Jiraiya leaves them about when they are Genin age (12-14) after training them for three years and then later on he trains the Fourth Hokage starting when Minato is 12, this couldn't work as the Ame orphans are 4.5-5 years younger than the Fourth Hokage. This is according to the data books. Nagato and Konan are 35 during the Pein fight arc while Naruto is 16 basic math indicates that they would be roughly 19-20 when Naruto was born, while Naruto's parents are 24 at time of death (AKA the night Naruto is born) and would've been 40 when they appeared in the cannon series if they had lived. So this fic is mostly how I think things would've actually worked if the If Jiraiya had found the Ame orphans after training Minato instead of before. As for making Nagato Kushina's little brother it only says that he lived with family and even on the wiki it says that they are presumably his parents with no confirmation which doesn't mean it's impossible, also this is fanfiction and I do what I want. Also I figured since I'm saving the Ame orphans, and Yahiko resembles Jugo enough for them to at least be from the same clan, having the same hair, skin, and eye color (eye color is kind of iffy since Yahiko and Jugo have different eye colors in the manga than the anime, and Yahiko is only ever seen alive in low light, but in low light their eyes look the same at least in the anime), so at some point Yahiko will start using Jugo's Kekkei Genkai. These aren't the only family trees that are getting fiddled with, the rest however are going to be revealed to the readers as the story progresses.

Prologue

"Well kids, I think I've taught you enough to survive. You're all thirteen now, that's official shinobi age, and I hate to say this, but it's hig8h time I get back to Konoha." Jiraiya says to the three orphans that he's been taking care of and teaching to live for three years. "Besides I think it's time for you to pursue your own goals." He continued.

The children in question simply stared at him before trying not to break into tears

"Sensei please take us with you. This land is war-torn and almost completely destroyed, we'd be much better off Konoha with you, even if it's the village that caused a lot of this destruction." Konan pleaded not wanting to live on the streets again.

"She's right, though I can't speak for Nagato since Konoha shinobi killed his aunt and uncle, I'd like to live in the village you come from, it sounds like a nice enough place. I would rather not live on the streets here if possible." Yahiko said looking at his best friend and rival.

"If I hold a grudge against an entire village for the actions of two likely dead men, then that would make me a serious hypocrite. I look to bring about peace and end the cycle of hatred. Honestly I'd rather have the backing of a major shinobi village than try it as a random group of teenagers that have basic knowledge of ninja arts." Nagato said standing from his seat. "Jiraiya sensei please allow us to accompany you to Konoha and live there. Besides if anyone from Uzu survived the attack I believe that that's where they would've ended up. Maybe I have family there."

"Well fine I'll take you with me, though it's up to my sensei whether or not you can stay. He is after all the Hokage. His word is law." Jiraiya says. "Pack your stuff, we leave in two hours."

The trip was not a quiet one. The orphan trio continuously speculating on how life inside a large thriving village would be. The three were understandably nervous, yet excited. Even living on the streets of Konoha would be an improvement to their life in Ame if they had stayed. As they crossed the border into Hi no Kuni the sun was so bright that they had to stop for a moment and let their eyes adjust to the light.

"It's so beautiful here. The blue sky, the trees, the sunlight. It's all a bit much to take in coming from a country where everything but the people is grey." Yahiko says earning confirming nods from his fellow orphans.

"Remember Nagato keep your eyes covered until we talk to the Hokage." Jiraiya said earning a nod from the boy.

The rest of the trip after that comment got quiet as the orphans soaked in the scenery of the land they hoped to call home soon. Jiraiya sent a messenger toad ahead of them to alert the Hokage of their imminent arrival in order to avoid any misunderstanding.

As they approached the village gates they were greeted "Jiraiya Sensei! How's it going? We heard you were on your way with company so we volunteered to serve as your escort to the Hokage's office." A tall blond young man of 18 standing with two rather stoic figures of the same age shouted at the group.

"Well will you look at that? The team's back together, after our trip to the Hokage's office we should go for some Ramen and catch up." Jiraiya said to the three as they entered the village.

"I can't after this I have a date to get to, and my girlfriend is the last person I want to piss off." The boy said scratching the back of his head and smiling.

"Really a date? Who with? Come on Minato give me some details here." Jiraiya's curiosity decided to show itself.

"You remember Tsunade's former student Kushina right?" Minato said noticing Nagato perk up upon hearing the name.

"You mean to tell me that you're dating the Red Hot-Blooded Habanero. How the hell did this happen?" Jiraiya was even more curious now.

"Well about a year and a half age she was kidnapped by five Kumo shinobi. She left a trail made of her hair and I followed it, I one of my new techniques to dispatch the kidnappers. When she asked me how I found them I told her that I followed her beautiful red hair, and we kissed. We later decided that it was likely a heat of the moment thing, but we decided to give dating a try, we've been dating ever since." Minato said giving the really short version of the story. "Come to think of it she told me that the Hair is a clan thing, this kid looks like he could be her brother." Minato continued while pointing at Nagato.

"Maybe. Last I heard my ne-chan was on her way here, but got attacked by bandits and killed along with Oka-san. Funny how even the third strongest ninja in a village can be killed by common bandits when they get careless. The only reason that I doubt that it's her is there were quite a few Kushinas in our age group in Uzu." Nagato said looking at the ground.

"Well I'll talk to sensei and see if some bloodwork can answer that debacle." Jiraiya says scratching his head.

"I'll send Kushina a toad telling her that I'll be late, she won't like it. But I think the sight of a cousin, or possibly even brother, along with my other surprise will more than make up for it." Minato said summoning a small toad and giving it instructions to seek out Kushina and tell her that he'll be late and that he'll give his reasons when they meet up.

"So Fugaku, Hiashi, what's new. Don't tell me that you two have girlfriends as well." Jiraiya wanted to know what his former students were up to.

"Well I made Jonin like Minato-san. And I have recently began courting Hitomi. Though my story is much less interesting than Minato-san's. We simply had mutual interest in each other and began courting as per the standard." Hiashi said showing no emotion in his face.

"I as well am now a Jonin, I will likely be clan head by years end due to my father's condition worsening. Not even Tsunade-sama can diagnose his illness, let alone treat it. And I also now have a romantic partner. Mikoto from Tsunade-sama's team will make a great wife, and mother someday in the future." Fugaku said remaining just as stoic as his longtime rival.

"Well I'll be damned. All of my team getting together with all of Tsunade's team. Who would've thought? Now if only Tsunade would finally realize that I'm not joking when I say that I've had feelings for her since we were Genin it would all be complete." At this point the group of seven had arrived at the Hokage tower. "Well this is our stop, I'll talk to you guys later when we can all meet up and go for ramen or something and catch up in more detail. Minato you should come with us. You are after all going to be waiting till we're done anyway. And the only secret will come after Nagato moves his hair." Jiraiya said whispering the last sentence in Minato's ear.

"Okay sensei." Let's go.

The way from the entrance to the Hokage's office was quiet with no words spoken. All present could feel how nervous the three orphans were.

Jiraiya opened the door to the Hokage's office saying "Sensei I'm home, and the three children behind me are the three orphans I stayed behind to train. Nagato apparently he's an Uzumaki, Konan, and Yahiko."

"Yes that one does resemble an Uzumaki. Do the other two have clans?" The third Hokage asked him.

"Not that we're aware of. Though that doesn't mean it's out of the realm of possibility. Konan developed jutsu revolving around paper, and Yahiko seems to absorb small quantities of Nature energy when his chakra is low. Now on to Nagato, I think that for this part it should be just us, the kids, and Minato." Jiraiya said getting incredibly serious with the last sentence.

"Before that, since they are here of their own free will I must ask. Why not just bring them here in the first place?" The third Hokage asked his former student.

"I didn't expect them to want to come here otherwise I would've just brought them here. Their parents and guardians were confused by Konoha shinobi for enemies and killed by them. Initially they didn't even trust me, being from Konoha this was understandable. I don't know when during the time we spent together they changed their minds, if I did we would've returned then rather than now." Jiraiya said before the Hokage waved his hand causing the ANBU present to exit the room.

"What about that boy is so special, and why trust Minato over my ANBU?" The Hokage wanted answers.

"Well we don't know if any of those ANBU are with Danzo, and Minato's one of the favored candidates for Hokage when he comes of age. Now as for what's so special, Nagato, show them your eyes." The boy did as instructed.

The Hokage and Minato gasped upon seeing his eyes.

"Is that what I think it is?" The Hokage asked jumping over his desk, scattering the paperwork, and grabbing Nagato's face. He then proceeded to turn his face examining the boy.

"Yes, that's the genuine Rinnegan. This surprised me as well when it awakened. I thought Kushina's chains were the Uzumaki Kekkei Genkai, but now, after learning that he is also an Uzumaki, I'm starting to wonder if they have two. Or maybe it's something more. We'll talk more about that later. My only concern is that he doesn't seem to be able to deactivate it. I mean it doesn't drain his chakra by simply being active, but it would be hard to explain if we had a kid walk around the village with the Rinnegan active." Jiraiya said scratching his chin deep in thought.

"Before we get too far off base according to Nagato he had a sister named Kushina, and he might be referring to my Girlfriend. Standard procedure for this situation dictates we have all three new village entries undergo bloodwork to see if they have any relatives in the village since they're orphans. I think we should do this as quickly as possible." Minato piped up reminding the others in the room the main purpose of the meeting.

"Yes we must get to that as soon as possible. For now, Nagato, use a Henge to hide your eyes. We'll find a better solution to this predicament later." The third Hokage said before letting go of Nagato and leading the group to the hospital to get the necessary bloodwork and exams done.

A few hours later

"Well Nagato, according to this chart your DNA is similar enough to Kushina Uzumaki to suggest that you share at least one parent. So in short she is indeed your sister. Other than that you are a little physically weaker than the typical Genin, but that can be fixed by adjusting your diet, and doing some more physical training. Your chakra reserves however are damn near off the charts." Minato said reading the results to the boy since the doctor had been called to a different patient whose life was in danger.

"So ne-chan is alive." Nagato was dumbstruck to say the least.

"Well that's all we need here for now. Let's get the others and go meet her, I'm sure she'd like to see you after all these years." Minato said putting the chart down and offering Nagato a hand.

"What if she doesn't remember me? What if it's awkward? What if the tests were wrong? I don't know about this." Nagato said obviously worried about talking to his sister for the first time in eight years.

"Well then we'll see when we get there. Come on Nagato even if she is just your cousin that's better than not having family period." Minato said helping him off of the exam table.

"That doesn't make me feel any better. I don't know what I'd do if the tests lied, I just don't want to get my hopes up for nothing." Nagato said with a frown.

"We'll see about that, first let's go see her. She's probably ready to tear my head off as it is." With that they gathered the other two orphans and left.

Several minutes later

Minato sent a toad to tell Kushina were to meet him and to be ready for two major surprises. He sat next to Nagato and the Ame orphans at Ichiraku Ramen. Nagato was wearing a traveler's hood in order to conceal his identity until Minato gave him the signal to reveal himself.

Kushina was fuming when she arrived. "You'd better have a damn good reason for postponing our date, dattebane!"

"Some business revolving around Jiraiya sensei's arrival kept me. These are the three orphans that Jiraiya has been looking after for the past three years. I decided to treat them to a meal before we figure out living arrangements for them. It seems that only one of them has a living relative in the village." Minato said while pointing at the trio.

"Oh yeah. Which one?" Kushina asked.

"Nagato you can take off the hood." Nagato removed his hood and turned to face Kushina causing her eyes to widen as if she'd seen a ghost.

"Nagato. Ototo." After saying this Kushina tackle hugged the boy so hard that he fell off the stool he was sitting on. "I thought you died when Uzu fell." Kushina was crying tears of joy while Nagato's face began to turn blue from lack of oxygen as he tried to return the hug.

"Kushina, you might want to loosen your grip, or else he might actually die from asphyxiation." Minato said both smiling and sweat-dropping.

"Oh Kami you've grown so much! Last time I saw you, you were just a cute little five year old." Kushina had allowed him to breathe, but was still smothering him with affection. He reached out toward Minato, his hand twitching. Minato could've sworn he heard the words 'help me' just before his Henge popped. Kushina felt the technique release and looked up only to notice nothing had changed except now the boy's bangs now covered his eyes. She tried to move them aside but found that Nagato was using the chakra sticking method to keep them there. "What are you hiding? It's not a hideous scar is it? Who hurt my Ototo? I'll kill them, dattebane!" Her hair started to form her trademarked 'tails' that put fear into the hearts of many.

"Kushina! Calm down it's not a scar. It is however something that can't be shown in public. Nagato resume the Henge, we'll show your sister later in private, now I think introductions are in order. Yahiko, Konan, this is Kushina Uzumaki, Nagato's long lost sister, Jonin of Konoha, and my girlfriend." The orphans nodded and waved when their names were mentioned.

"Nice to meet you Kushina-san" Konan said before creating a bouquet of paper flowers and handing them to Kushina.

"Don't mind her, it's just her way of extending the hand of friendship, kind of like a handshake. She can be a little weird like that." Yahiko said while staring at the menu.

"Well then, thank you Konan. So you guys have been living with Nagato-kun for a while now." An awkward silence fell upon the group that lasted for almost a minute before Kushina tried again. "Do any of you have any clue where you are going to stay?"

"We'll figure something out, we always have. Even if we live on the streets it'll be an improvement from Ame. At least here the weather is nice." Yahiko said trying to reassure himself more than anyone else.

"Well, if you can't find a place to stay, I've got open rooms that you could use until you can find a place to stay." Minato said throwing out the offer.

"Minato, did you hit your head or something? Last time I checked you lived in a one bedroom apartment like me." Kushina was earnestly confused.

"Well that's something I wanted to talk to you about. We've been dating for more than a year, I was kinda wondering if you wanted to move in with me? I bought a four bedroom house earlier this week." Minato was acting kind of shy, Kushina found this to be cute.

"Minato, I would love to move in with you. But first, why four bedrooms?" Kushina already knew the answer, but she wanted to hear Minato say it anyway.

"In case of family expansion, you know, kids." Minato was blushing furiously when he said this, as they have yet to even perform the act required in order to make children. Let alone plan for what to do if they had little ones running about.

Kushina pulled him into a kiss a few seconds after he finished speaking. It was brief since they were in public, PDA wasn't really their thing.

"Well let's eat, then we can figure everything out later. I figured that I'd at least extend the offer." Minato said before ordering

AN: That's it for now. Tell me what you think so far. Am I doing good? Should I continue, or should I make this fic disappear? I really want to know what you people think. Anyway leave a review answering these questions, and I'll see you next time, if you stick around that is.