Resistance is Magic

by ColtKit Productions

Chapter 1: Planning for the Future

4 Years ago...When the Borg came to Shinobi World. They were unaware of the trouble these primitive lifeforms would cause. While the species seemed to have rudimentary technology, what attracted the Borg was the high levels of unrecognizable energy, coming off the planet. The readings were intriguing. It was definitely something worth adding to the Collective, despite the low levels of technology.

They used their specialized Tractor Beams, to carve out the ground around several cities, and brought them onboard their super cube vessel... that was their first mistake... the next was trying to jettison the cities into space, when they realized they couldn't be upgraded... They would have left the planet in peace at that point... but the humanoids fought back... the next mistake was, after the Borg realized how dangerous these "Shinobi" were, they disintegrated the planet...

That is when the "Jinchuriki" on their Cube vessels became so distraught... their demons took over... the Borg never stood a chance. Every last drone was torn to shreds, to the point not even their nanites could repair the damage... Their Borg Queen onboard, transmitted the records of the incident, to the other Borg Queens... and it was decided... all beings with Chakra must be purged, for fear they could end the Collective.

Then... they found Equus...

###

Naruto yawned as he woke up in the Hokage Tower. The one and only good thing about the Borg attack is that Sarutobi, the leader of the village and honorary grandfather to "The Demon Brat", told the clan leaders they could shove it (though in less kind, and more fancy, words). That every reason they had to keep Naruto from him was no longer valid. So the Hokage, honorable leader of Konoha village, brought Naruto into his home...

Naruto used to live in an orphanage... and then a cheap ass apartment after that matron kicked him out... Now he lived in a near palace, with literal servants catering to his every need. Though Sarutobi was making sure that didn't spoil the boy. Naruto was expected to clean up after himself... or at very least put his dirty dishes in the sink, and not leave them lying around.

Since the Borg attack, when Naruto was just 8, the Hokage had been raising him. Even training him, and making sure the Academy stopped trying to sabotage the boy's education. Even had a few instructors imprisoned if he recieved proof of such abuse of power.

Sarutobi had told Naruto why the villagers hated him, and upon the boy's pleading, removed the law to execute people who dare speak the truth of it. Naruto... was a Jinchuriki, a host for a demon. Sarutobi was adamant that Naruto was just the vessel, the prison, and not the demon itself... Of course the man kinda had to explain this, after the Borg attack, as the rage of the demon had resulted and Naruto, and the other Jinchuriki, massacring the Borg.

But Sarutobi was able to talk the boy down afterwards... and Naruto just ended up crying in the man's arms...

Later the man told Naruto everything about his past... and regaled the child of stories about his father... the last Hokage... that had been a shock... that knowledge had been kept secret from Naruto before the Borg. To keep him safe from his father's enemies, and to not poison the newest Generation... though that last one didn't work so well...

Ironically, it wasn't til knowledge of the Kyubi became public, did the other kids stop picking on him... most still didn't like him, but he had grown closer to his friends.

Naruto sighed, getting up and out of bed, stretching his arms. He needed to get ready for another long day of D Rank missions.

After the Borg, most Shinobi missions had less to do with protecting, and more about surviving. Stuff like helping out the farmers and making repairs to the city... and learning all they could about the ship they were in... though that last one was mostly left to the older, more experienced, Shinobi.

When they joined the ponies... who, SOMEHOW, expanded this cargo bay to be an exact replica of the entire Elemental nations' continent, down to the varying weather patterns. It was the most complex of all the pocket dimensions. As the others merely had one, consistent, environment.

Oddly enough, all the Shinobi clans, from all the villages that had been taken, built their new homes in private estates, but kept them in the same village. This giant neighborhood was divided into estates based on clan... As most the civilians had been killed by the Borg... and a good few of the Shinobi as well... in fact, the only Kage to even survive the attack... was Sarutobi. So it was pretty easy for him to Convince the clans from rival villages to help him rebuild.

These past few months, they had the Shinobi helping the other races build homes in their various pocket dimensions. Captain Janeway even had the Jounin rank Shinobi working alongside the ship's "Security Officers". Doing what they were originally trained to do. Saving lives and fighting bad guys... It was a good life.

As these thoughts ran through the spiky haired blonde's head, he finished getting ready for the day. Now, to breakfast with the old man.

###

Itachi wanted to grown, rub his temple, anything that could alleviate the frustration of... paperwork...

Sasuke was snickering at him.

"I would watch who you're laughing at, little brother." Itachi warned, without looking up from the papers. "This could be your job one day."

Sasuke snorted from his place at the table. "Not likely, hurry up and pump out a kid. Then it will be their problem."

Itachi couldn't resist rolling his eyes, "I'll have you know, as soon as your of age. I could step down and have YOU deal with all this."

Sasuke paled, "You wouldn't."

"Don't tempt me." Itachi warned.

"Must you do that at the breakfast table?" Mother eyed him disapprovingly, as she laid their breakfast on the table. "I don't want you to get into the same bad habits as your father."

Itachi flinched. It been 4 years... and he still hadn't gotten over what his father tried to do. Luckily, the man had been killed during the Borg attack. Itachi had inherited the role of clan leader. Then he instantly squashed all thoughts of taking over the village. Seeing as they had been struggling for survival, on a derelict space ship, it was an easy enough notion to crush. All without alerting the Hokage the great house of Uchiha had been planning to betray their own village...

Itachi actually had the elders of the clan executed for suggesting it, then appointed a new, slightly younger, council. People he could trust, ones that had been actively against turning on the village... and who Father himself had been planning on taking out.

Father really was a bastard. Itachi didn't like being compared to him in any way, and Mother knew it.

The young Head of the Uchiha Clan, put his papers to the side, and began to eat.

"So you and Sakura going on another date?" Itachi, not so innocently, asked. It was his turn to tease.

Sasuke scowl. Then muttered to himself, "I can't stand that bloody fangirl."

Mother smiled at Sasuke, "Speaking of potential girlfriends. I noticed you spending a lot of time with that Applebloom girl." Sasuke froze, and their mother instantly noticed. "I think she's a lovely girl. And that Earth pony magic might be something worth while to add to the Uchiha clan."

Sasuke relaxed some, but sent a worried look at his older brother.

"Some people may be critical of an interspecies relationship," Itachi didn't bother sugar coating it, but neither did he have any desire to be cruel. "However, It's only natural they pop up, given our close quarters... The apples are a worthy clan to affiliate with the Uchiha." he gave his blessing, and Sasuke smiled... so Itachi felt comfortable teasing again, "Should I speak with her family matriarch, and arrange a marriage."

Sasuke's face turned the most delightful shade of crimson.

Mother simply pointed out, "Bit early for that."

###

Twilight frantically burst into the Observation Room. Janeway was almost used to how easily panicked the young woman became. She was only a minute late.

The Bipedal pony quickly saluted... as she seemed to have forgotten Starfleet didn't do that. "I'm here to give my monthly report, Captain."

Janeway gave a curt nod. "If your ready, we can get started."

Twilight teleported in front of the screen... the girl really wasn't one to waste time. Even the measly seconds walking took up.

Twilight looked around the room at the Senior Staff of the Federation crew. The kind creatures who dragged their tree in a "Tractor Beam" around the sector. Who took time out of their urgent schedule to backtrack the planets they had visited, in order to convince another world, any world, to accept them... and when none had, these creatures had offered to take them in.

This entailed plans to extend the shields, in order to create an environmental bubble of heat and oxygen. While they continued to use the tractor beam to drag the castle back to Earth. This would have slowed their speed, making the trip take over a humanoid's lifespan of a 150 years, but the crew was willing to do it... just because it was kind...

This crew was trapped in the Delta Quadrant, via alien abduction (Which Twilight was shocked to learn actually happens, even to advanced aliens)... they were trying to get home, which was on the other side of the Galaxy... they had been stranded near a year themselves... yet they were willing to never make it back home, in their lifetime, just to help another group of stranded aliens...

Obviously, not every creature could live on the ship... not originally. There were just so many Refugees, about 5 thousand per species, that it be impossible for the Voyager vessel to hold every creature.

After Janeway made the offer... while the first thing that happened was the "Dilithium" castle exploded. While that had been devastating at the time, as the Princesses thought the last of the survivors were lost... but they soon discovered a large surge of magic, which they followed into an empty deck, filled with even emptier cargo bays.

The crew explained these cargo bays were designed to hold survivors from large scale evacuations... and had discovered that when the tree exploded, and Voyager got caught in the blast, that the largest of the bays had the Castle's pocket dimension attached to it. The Pocket Dimension, formerly anchored inside the Castle, was now attached to this cargo bay. Then the other Cargo Bays had other dimensions anchored to them. One for every race of creature, tailor made to their most comfortable environment... all the size of... while the Humans compared the land mass to "Australia"... which was apparently a continent on their planet.

The Map had somehow known about the bay. Though if creatures were going to start questioning how the Cutie Map knew things, it really should have begun a while ago.

It should have been impossible. The castle's pocket dimension was the size of a small town, PER FLOOR. It was already irrational that it fit inside the castle at all!!!... but then it was almost as if the Castle knew they would need saving, and that was the reason it was so large.

Just before their planet was even aware of the danger it faced, the Cutie Map had summoned every creature it could possibly hold, from races all over Equestria... It knew... and it saved as many as it could... enough from every species on the planet, so they could regrow a healthy gene pool... though billions still died... but where was Discord.

Yes, as a higher spirit, it was laughable to assume he would get involved with every conflict on their planet... but... Twilight had grudgingly begun to think of him as a real friend... she knew he cared about them... yet he let their planet die?... why?... just... WHY!?

He could have sent the robot zombies away with just a snap of his fingers... yet he didn't... he let billions die...

Not even Fluttershy could figure it out... and she hadn't seen her friend for moons before the attack...

Twilight sighed. This wasn't important, at least not at the moment. She needed to give her report to the Captain. As the Princess of Friendship, the new Council of races had elected her as the liaison to the crew.

After some negotiations, the Federation President had promised to give the Equines the ship... after the safe return of their citizens. Until then, Janeway was in charge.

Yes they had their own civilization rebuilding within the pocket dimensions... but the ship it was attached to belonged to Janeway. As such all of the Refugees could consider themselves drafted. Which really wasn't a problem. The various races of Equus understood what a large favor Janeway did by accepting them... and not freaking out too badly that the Castle Dimension had attached itself to her ship.

The President even told Janeway that she should considered the entirety of the Refugee Deck as belonging to the races of Equus. The Refugee Deck was now consider Sovereign territory, where the races could grow as they see fit. Still Twilight was expected to give reports on what they were doing.

"The last of the houses have finished Construction," Twilight explained. "Thanks to the trees the Earth ponies have managed to grow. Those red wood seeds, you replicated for us, really came in hoofly. The Earth ponies were able to grow them to full maturity within a week, then treated them for proper building material. As of now, all races have permanently moved out of the Castle.

"The only people actually living their now; are the ambassadors, the guards, and the servants and staff.

"It was decided most floors would be turned into farms, ranches, and wild life preserves (for the magical beast, and Domestic animals, we managed to save). As well as a laboratory set up on another floor, for magical and scientific advancement.

"Oh!" Twilight grinned, "We finally got an education system agreed on, and have finished remodeling 4 floors in the Castle, strictly for education. The children have even begun their first new school year today!!!" She clapped her hands, excitedly.

"We also confirmed our suspicions that the Shinobi's form of magical manipulation. Which they call 'Jutsus', can be taught to any magical being. While they were adamant this style of magic should be taught to young children, we were able to convince them to integrate into our own educational system. Where Children of all species, from 3 to 11 years old, learn all the basic academics. Then they move on to classes separated by species, or clan. To study their racial magics, which the Shinobi refer to as 'Bloodline Traits', until they are 15. At which time, they rejoin all races, in order to study at a university, until they are 25.

"However, they can join an apprenticeship at any time. Including studying Jutsus as an after school activity. This program will now be necessary to join the Guard.

"However, on the Shinobi's insistence, Any student far enough into this program, usually at age 12, will be placed under a Sensei. Who will give more specialized training, based on the student's aptitude and the Guard's own specialization. These students will even be allowed to assist with 'D Rank Missions'. Which are basically chores around the pocket dimensions. As they study for their future field in the Guard.

"Fields such as Tracking, Healing, and all the Positions onboard a star ship." Twilight looked at Janeway. "The Council would like you to teach these, magic school aged, children how to operate the ship, along with the adult guards they are already educating."

Janeway frowned, "Normally, I would speak against training such young children, on how to operate a star ship. However, as your Society is quite literally bound to this ship, it may be prudent to have as many trained officers, as quickly as possible... As Either way, the children are trapped on the ship."

Twilight smiled, "Thank you for understanding our position. And rest assured, we will attempt to keep the children out of any potentially dangerous assignments, such as the away missions."

At Janeway's nod of understanding, The princess moved on. "Next we made our own Social floor, which your crew is more then welcome to use (and some have), on the same floor as the Library. We have a few movie theaters set up in those rooms, a bowling alley, an arcade, a small water park, and several other areas for recreation and socializing.

"The Minotaurs and Griffins wanted a... a 'Red Light District', but it was thought best to cover that into an entire floor, instead of having it somewhere that children could get to. We have an age line to prevent children from stepping off the stairs, into this floor." Her cheeks were pink, and she attempted to slide right passed it... unfortunately Second in command Tuvok was curious.

"What exactly is a 'red light district'?" He asked, "And why would it need be inaccessible to children?"

Twilight blushed, thankfully Janeway spared the girl, "It's a place were people can experience their vices in a safe environment, away from tainting innocent eyes. Where they partake in gambling, drinking, sometimes drug use... and prostitution."

Tuvok raised an eyebrow. Then turned to Twilight, "I can see why you would want to keep this out of reach of children."

"IT WASN'T MY IDEA!!!" Her voice hit an impossible octave.

"Lieutenant Paris," Tuvok turned to the primary pilot, "Perhaps this place would interest you."

Tom Paris flashed an unrepentant smile, "I'm sure I'm not the only one, but just too be clear." He looked at Twilight, then asked, possibly just to mess with her, "The Prostitutes are real right, not holo characters?"

Twilight's face turned bright red, "Well, they aren't really prostitutes. We have a few gentle mare's clubs. Where willing adults are paid to flirt and act as a form of emotional support. They are trained, and licensed, 'Companions' that do a lot more then just have sex for money.

"But they still have sex, right?" Paris grinned.

Janeway choked back a laugh, "That's enough Tom, stop teasing the girl."

"T-teasing?" Twilight blinked, then glared at Tom, "Honestly!!!"

Tom just laughed, "Is it my fault your so easy to windup?"

"Did you do anything else to the castle we need to know about?" Janeway asked, already knowing the answer.

"Well," Twilight sighed, as she gathered her thoughts. Poor girl was still a tad flustered. "... yes," she said, after a moment, and thankfully the rest of the Senior staff let her calm down, sensing they might have been pushing her too far. "A few things. We converted many of the Floors into 'Market Districts'. Just regular old markets, where ponies can start trading goods with each other again. We realize the Federation doesn't have a traditional economy, so our merchants would be willing to accept Replicator Rations for their goods."

"Why have money at all?" asked Chief engineer Torres. The woman had a bit of a temper, which she was struggling to control during Tom's lewd jokes. Her Klingon heritage was a nightmare to handle... but she tried her best not to scare the easily frightened ponies. The other races they had taken onboard weren't so easily intimidated, but the ponies were a jumpy lot.

Twilight sighed, "We grew up with using money to motivate our citizens. Every creature simply acting for the benefit of survival... as left a sour taste in our mouths. We want normality. So an economy where individuals are rewarded for their hard work, beyond just acknowledgement of a good job..." she tried to gather her thoughts, "It's something tangible. We are tired of working for the sake of living, with no goals beyond surviving to the next day.

"We created a digital based economy. Meaning we can pay people an unlimited amount of credits, for working, while also making it so all necessities are free. Every creature now carries a credit chip, which doubles as an ID, down to their profession and position, and has any licenses they may possess.

"They also keep track of their food allowance and their toiletry allowance, two separate things. However, in addition to that, they can buy extra food or any other luxuries they might want, with currency. Our economics operate as a more compassionate version of capitalism. Where any creature can aspire to new heights, but are guaranteed the necessities, even if they fail. Hopefully, future generations will agree our system is a less extreme version.

"Our team of enchanters have also finished upgrading the shields, and the density of the ship's hall. Through simulations on your Holodecks, we speculate the Ship could now survive a close range supernova. This means, the weapons of other ships, are all but worthless against us. Unfortunately, as I warned you earlier, the ship is now more vulnerable to boarding parties, as all resources were spent insuring the ship cannot be destroyed... It's more likely creatures can 'Beam' in with this upgrade. Luckily, few have that ability in this Quadrant of space.

"Also, as suspected, the force fields around the windows and the shuttle entrance, are better at keeping in the atmosphere, but it is more likely matter will pass through it. Just tripping won't do it, but with enough force, anyone can fall over board. I highly suggest creating a barrier of enchanted, unbreakable, glass, to go over the force fields of the windows. Then stationing more guards around the Shuttle bay. As anything from meteors to intruding ships can easily break in.

"While these upgrades make us more sustainable to onboard attacks, they also insure the ship will survive, no matter what. Hell, simulations suggest we could survive traveling through a black hole... with the shields up at least.

"We have also succeeded in building our own type of Faster then light engine. Combining Federation technology, with our understanding of magical flight, this engine can lower the mass of the entire ship to that of a single light particle. Then move as a wave, through warp, to travel at approximately 167.94% more efficiently then traditional warp... With this we can go faster then warp 10, without approaching the nightmare that is transwarp. Thanks to the magicals Upgrades, the ship can easily withstand this speed at a consistent space."

"How quickly can you have it installed?" asked Harry.

He was a young Ensign that somehow found himself on the Senior staff. Though it was hardly a fluke. The boy showed a real talent for "Thinking outside the box", that he was trusted with a position on the Senior staff, despite his rank. And now that they had so many new aliens studying starfleet protocols. The Boy might very well get promoted, once the new officers completed their training.

"We'll need to find somewhere safe to park, remove the current warp engine, and install the new Magical Engine... it should take about 3, Federation Standard, weeks."

The Staff nodded. While Janeway said, "We'll begin looking for a peaceful port immediately. Though, staying still for so long could attract the Borg."

"Our concealment spells should keep us hidden from their sensors," Twilight assured. They talked about it for a little while longer, until Twilight was allowed to move on with her report.

"In addition, we made a brave new discovery about the Pocket dimensions themselves. When the castle exploded, it, didn't actually create any pocket dimensions. These dimensions were already in existence, at the surface of sub-space. The explosion of magic, merely allowed the Tree of Harmony to link the dimensions to existing points in our universe. She obviously planned this, as the environments were clearly carefully chosen, for each species."

Tuvok looked intrigued again, "How did you determine this?"

"We found Fossils!" Twilight hopped in place, giddy as a school girl. "Millions of years old, in fact. These dimensions have clearly been around awhile. This shows that the animals that inhabit these dimensions, properly evolved there, and didn't just... SPRING INTO BEING. Even the tree has limits, as she clearly had to anchor preexisting dimensions, as opposed to just creating continent sized ones."

"Isn't it possible," Tuvok probed, "These, pocket dimensions, have other intelligent life within them?"

"That's extremely unlikely," Twilight dismissed. "Firstly, while we have found fossils, there is no proof of anything resembling intelligent life. No tools or ruins. Second, we have had our best Pegasi teams flying around, mapping the continents, and nothing. Third, I highly doubt the tree would give us land just to turn us into accidental conquerors."

Tuvok raised an eyebrow, "You put a lot of confidence in this... tree..."

"Well... The Tree of Harmony is a self aware pocket dimension. It had been trying to communicate with our world for centuries. Initial contact was made by Star Swirl, and given a presence in our Dimension in the form of a Crystal tree. As the tree watched us, it tried to get more and more sustenance in our dimension. Which it's connection to myself, and my friends, unknowingly provided. When we proved ourselves to the tree, it was able to grab a firm hold in our dimension. Creating the castle as it's doorway.

"Can you comprehend such an intelligent entity? A living dimension, that has been protecting and shaping our planet for over a millennium? To the point it saved all it could during the Borg attack? For whatever reason, this entity has chosen to help us, to the point it anchored itself to this ship. It obviously took a great deal of magic to transfer the link, and it clearly can't just open up wherever it wants. It has limits, we are finally starting to learn what they are. It's even possible that the other dimensions it grabbed are also self aware. Maybe even it's friends or family. Then again, they could just be ordinary pocket dimensions. We need to run test for cosmic brainwaves. We are even developing a way to SPEAK with the Tree!!!"

The Captain looked worried at that. Having a dimension anchored to her ship was mind boggling enough... but the fact it was also a self aware entity. One that appeared to have heightened awareness of their own dimension... she would have to report this to the president.

"Why didn't you tell us sooner that the dimension was ALIVE?" Paris showed his usual level of tact.

Twilight stared at him, confused...

"She did," Janeway sighed. "All the Equusians have been talking about the dimension as if a beloved friend. We merely assumed this was more a sentimental attachment... we should stop making any assumptions about magic. We simply don't have the level of comprehension needed to do anything of the sort." Then the Captain looked at Twilight, "And you need to do the same. You're explaining concepts we have no basis for. Don't assume we know what you mean about ANYTHING. This level of miscommunication cannot be allowed to happen again."

Twilight straightened, "Yes Captain! It won't happen again!"

Janeway got the impression the girl would now recite everything as if reading from a children's text book... joy...

###

Kabuto sat in his room, listening to the whispers of Orochimaru in his head. Those loyal to the sound Villages had been given their own estate, and the full rights of a clan... that is, after Orochimaru was sealed and his host made the head of the clan (by the clan).

Kabuto wasn't expected to survive the sealing. People over a certain age couldn't withstand having a demon in their belly. Their bodies would quickly deteriorate and they would die. However, the snake demon, Orochimaru, had accepted it's host for "Unknown reasons"... but Kabuto knew.

Orochimaru didn't want to die. Orochimaru might be a snake in appearance, but he was a leech by nature. He couldn't survive without a host... and at least this way he had a host that wouldn't deteriorate. A host that was loyal to him.

Orochimaru might not have direct control, but Kabuto still listened to his orders... and was biding his time.

"My Lord?" the pale face of Kimimaro stepped into the room.

The ponies had done what not even Orochimaru could do... what not even the healing or Necromancy Jutsus of Kabuto could do... they cured Kimimaro of his bloodline sickness. It was basically a type of cancer that manifest through the genetic powers some clans are born with... and the ponies cured him... Obviously, he was conflicted with Orochimaru's plan.

The ponies appeared to have Bloodline traits, related to their species instead of family clan. Yet they could stil learn Jutsus. Some of the other species had similar "Magics" as they called it. But the Ponies were of particular note... especially the Unicorns, who's bloodline trait allowed them to bend reality to their will.

Kimimaro looked grim, "Our Spies inform us that the crew will be turning off the warp engine and installing the Magic based Engine... We will be parked in a nearby nebula for 3 weeks."

Kabuto smiled, but it wasn't his usual condescending grin... this smile was more... predatory. "Then this may be our chance to take control of the ship." He really didn't know why the aliens wanted to help these lifeforms "get back home". Or even why they were letting them call all the shots. Hell, even that worthless Hokage was in agreement on that... But not Kabuto, not the Sound 'Clan'. In the past few months since they joined, they had learned everything they need knowing about operating the ship. Now the Terrrans, with their small eyes and bland hair colors, were just going over the thousands of protocols this 'Federation' had...

But the Sound clan had gathered allies. There were several disgruntled individuals, amongst each species and even the Shinobi clans. They all believed, as Kabuto did, that they shouldn't waste time getting these aliens back home.

They should be using all their resources, into fighting the Borg. Then, once every last Borg was exterminated, they could focus on joining the political squabbles of the other planets. Acting as more Nomadic warriors for hire.

They didn't need the Federation. They didn't even need a planet of their own... not with their current resources

Kabuto suddenly frowned, as he heard a whisper no other could hear. "While this was certainly a golden opportunity to attack the Federation Crew," hissed the voice. "We haven't built up enough allies amongst the other races. The guards would certainly try to stop what meager forces we have."

"This is one golden opportunity... we must let pass us by," Kabuto didn't comment on Kimimaro's relieved expression, "Orochimaru believes we need the other races on our side, before we make our move."

"God is wise," Kimimaro stated.

Kabuto did his best not to snort. Orochimaru may have stepped beyond human limitations, but he wasn't a god. Hell he was probably the exact opposite of a god. He was a demon, though born a Shinobi.

"We must bide our time." Kabuto translated the hissing voice he heard. "Even with the Magical Engine, it will still take us over 20 years to get to the Alpha Quadrant. We have time to spare. Once we are ready. These Federation simpletons will die... and if we follow Orochimaru's plan, it will be with the Ponies blessing."