Edit: as of November 2021.
I separated this from that last chapter, to make it flow better.
Nagato... had been a victim of war. His family were just civilians. Uzumaki, living outside the clan, strictly for the purpose of trading with other clans... his parents were just common merchants... they were killed by some trigger happy Shinobi from Konoha... they had been mistaken for enemy Shinobi, and killed without so much as a request to identify themselves.
Nagato had been slowly starving to death, ever since... until he found Yahiko and Konan... other kids, orphaned by the war...
They had been stealing food for near a year, before Yahiko got this crazy idea to become stronger. Strong enough to put an end to war... Nagato didn't dare say it... but he found that really circular thinking.
How could more violence, somehow, end violence? Regardless, Nagato followed... As Yahiko had accepted him into his hiding place. Kept him fed and protected him... even if the Uzumaki didn't understand... he would have followed Yahiko to hell itself.
Konan seemed to think they could do it... that they could become strong enough to end the very idea of war... she bought every word.
They both followed Yahiko, out of their hiding place, and into the middle of the war... and found a Sensei.
Jiraiya stood up. The children just blinked at his sudden stiffness. They had just sat down to eat.
Then they felt it. The wind picked up, and a light Flashed.
Nagato gaped, quickly standing as well. "A TARDIS?" He watched as the vessel slowly faded into existence. Even as a Civilian, he could recognize the war vessel of his clan.
Jiraiya slowly nodded, relaxing a good bit... but somehow even more tense. He had received Messages, by way of carrier summons, about how the Refugee Uzumaki had officially been granted a clan in Konoha... That had actually ended any chance of the peace talks with Kiri...
Regardless, the Uzumaki would be here on Konoha's behalf... likely to get Jiraiya to abandon the kids and return to the front lines... maybe, given Nagato was an orphaned Uzumaki, Jiraiya could convinced the people to take all three children into their clan... that would, realistically, be better then living in a roofless shack in the middle of a war... even if he would lose them...
The TARDIS became solid, and a scrawny man, with quite the fashion sense, strolled out... he had the same ripple eyes as Nagato... hopefully only activating those, because he wanted to lay all his cards on the table... and not because he was ready for a fight.
Someone else, an older teen, walked behind him. With one ripple eye and one Sharingan, slightly hidden by the orange goggles he wore. The first man just raised his hand, and the boy immediately stopped.
The man flashed a goofy smile to the boy. "Wait with the others," he ordered. "No sense overwhelming them with a herd of people. You can watch from the monitors... if anything goes wrong. Don't come out. Just get the TARDIS out of here. I'll meet you later." The man was sure confident, before a Sannin.
He gave a little skip, then, hands in his pockets... likely clutching a weapon, he stride over. The doors closing behind him.
Once the goof of a man reached them, he simply informed. "Message, From The Yondaime Hokage," he grinned.
Jiraiya stiffened. A message? From his former apprentice? It was one thing for the Council to order him back to the front lines... but he couldn't imagine Minato ordering him to abandon kids...
The scrawny man fished out a scroll from far too small pockets. That didn't even phase Jiraiya. It was a common seal to add to pockets, making them bigger on the inside.
What did surprise him was this man was a messager. The Uzumaki was trying to hide it... but he reeked of power... this guy should be fighting, not delivering messages.
Regardless, Jiraiya took the letter. The man just stuck his hands back into his pockets. Then began rocking on his feet, as he smiled...only someone used to war could be so calm here. True, they were a good few miles away from the battles, but they could still hear the explosions and screams echoing.
Jiraiya cautiously opened the scroll, one eye reading while the other studied the man. Ensuring the man wasn't going to try anything.
Jiraiya startled, as he realized these were transfer orders. He sent his Chakra through the letter, and confirmed it had been written by his former apprentice. It matched his Chakra signature.
The letter informed that the man was the 'Captain' of a new black ops team. Part of their agreement to let the Uzumaki join the village. He was a non combatant diplomat. Though Minato assured he could hold his own if he absolutely needed to fight... Minato informed that this man, at the request of Lord Uzumaki, had been allowed to choose his own team... and Jiraiya was to go with him... with his knew apprentices... They were to be brought into the Uzumaki Clan... and as such, given full citizenship in Konoha... and Jiraiya was to be their official Sensei, with the kids being recognized as Shinobi of The Uzumaki Clan...
This was better then he ever expected. Not a month ago, Minato made it clear, the Council wouldn't grant the kids citizenship... but now that they were accepted by a clan...
Jiraiya looked back at the, rather goofy, man... He didn't look entirely sane... which only confirmed his role as a seasoned Shinobi. You didn't see all the horrors of the world, and keep your mind unscarred.
"Pack your things kids." Jiraiya set the scroll on fire, as was protocol. "We're going back to Konoha."
Yahiko stiffened. "We aren't leaving our home!"
Nagato looked like, the hope he was feeling, suddenly shattered apart.
"The whole point of training, was to be strong enough to save our country!" Yahiko insisted.
The, not quite sane, man shrugged, "You can always come back, after your training is complete. Your recognized as Uzumaki Shinobi, not that of the village. That will allow you more freedom. Lord Uzumaki, has given his word, that as soon as our team is strong enough, we will be acting as a relief force for the civilians of Rain Country."
Yahiko's eyes widened. They wouldn't be killing soldiers for the sake of bureaucrats... they would actually be helping the people... this sounded too good to be true.
"Why?" Yahiko glared.
The man took his hand out of his pocket, and pointed at Nagato. "The first natural born, with the Uzumaki bloodline trait, in 27 years." He put his hand back into his pocket, "Lord Uzumaki might have awoken our bloodline trait, but young Nagato is invaluable to our clan. He holds the purest genes."
Nagato... gulped, "Lord Uzumaki... has returned?"
The man just shrugged, "He seems to mostly keep to himself. When he isn't assaulting Hyugas."
Then moved on, looking back at Jiraiya. "Due to the war, we lost contact with many of the merchant families, that were living outside the village. Many of them were trapped behind enemy lines, and we couldn't use our TARDISes to get them out... not without risking them."
Nagato nodded, as an Uzumaki, he understood that the safety of a TARDIS came first. The poor things were all but helpless, without a Shinobi onboard. Shinobi could pump their Chakra inside, to fuel the weapons and shields, but without them... the TARDIS was just a wooden box... a wooden box containing a merciful entity inside it. TARDIS were pure, Nagato might even go so far as to call them "Innocent"...
While simultaneously being the most dangerous weapon the Uzumaki Clan possessed. Even more dangerous then a fully manifested wielder of the Uzumaki Bloodline... which now all of them possessed. The entire mega system would be threatened, if a Village like Kiri, got a hold of a TARDIS...
So even if that meant leaving the, occasional, child to die... The TARDIS was too important to risk... and the Uzumaki clan couldn't get a rescue party this deep into the war, any other way.
As Nagato thought on this, the man continued to Jiraiya. "Your reports about stumbling on an Uzumaki orphan, of just what he's been through... it's of great shame to my clan.
"We are willing to accept his friends, in an attempt of making integrating him, back into our clan, go more smoothly. It wouldn't exactly help his image of us, if we just dragged him back, and forced him to abandon everything he loves. Such few things are precious in a place like this." He looked around at the decrepit shack, and towards the sounds of death, only a few miles away...
The man sighed, "As I said, a great shame one of ours grew up in a hell like this."
Konan looked at Yahiko, who still looked worry. Nagato gently touched the other boy's shoulder. Using his finger tips, instead of his palm. Yahiko looked at the red head.
"It's my clan..." was all Nagato said... but Yahiko could still hear the hope in his voice... as if he believed them to be saved.
"Fine." Yahiko caved. He still didn't like this... but Nagato had trusted him with so many things... he couldn't reasonably ask the boy to abandon his clan.
The oddly dressed man clapped his hands, "GREAT!!! Off we go."
As the man turned Jiraiya informed, "We need to pack first."
The man blushed, as if he realised he had forgotten such an important thing. "Right!" his face turned a deeper crimson by the second.
"We don't have much," Konan decided to speak up. She was a pretty quiet girl.
The adults nodded, as the kids ran into their shack. Quickly packing what few treasures they owned.
Jiraiya, and his officially declared Genin, walked inside the Pocket dimension. Nagato was eagerly explaining the basics of such inter dimensional Physics. Though the group was too awed to listen.
They walked through the engineering deck, and into the officers' wing. Towards the very back, there were about 8 condos. 4 on each side, and a private bathhouse at the end of the hall. All for the Senior staff, and their apprentices.
Occasionally, their "Captain" would shoo away some of the crew... they were all so young... eager to meet the Sannin... eager to geek out about all the things the Uzumaki could teach them... but the Captain kept insisting they needed to let the new guys get over the "Culture Shock" first. Jiraiya was grateful for that.
About the only people they were actually introduced to, was the "Senior Staff".
However, the Three Jonin, none of them even out of their teens yet, were quickly sent off, after introductions were made. With a command to pilot the ship back to The Uzumaki Compound.
Leaving Team Jiraiya with, "Tsunade!" Jiraiya grinned, finding his teammates, who remained near constants to him since he became a Genin. "O'chi." Jiraiya patted the pale shoulder of his best friend, Orochimaru... who scowled at the use of a nickname.
While their Sensei got reacquainted with his childhood friends... that he left to train his new Genin. Nagato watched as the Captain stepped into his own Condo... and the boy caught sight of it. In the corner of the Captain's sitting room... was another blue shrine... A TARDIS in a TARDIS.
Obviously all Shinobi, back from the days of Hagoromo, knew how to get around the issue of putting an expanded container, inside another expanded container. It's how they could put storage scrolls inside Storage Scrolls... but this... this TARDIS... It had small windows, and writing on it... "Police Public Call Box".
Nagato gulped, and hesitantly looked over at the "Captain". The man just smiled at him, before slowly bringing a finger to his lips. Making the universal "Shhh" sigh, as the door closed.
Nagato hesitantly nodded, gulping again... not planning on scaring his friends... their Captain... was none other then the ancestral god of the Uzumaki Clan... whatever this crew was chosen for... well... it wouldn't be boring.