Pokemon: Nova Aetas - The First Journey

by Mkchief34

Rating: teen
Tags: Other, Romance, Adventure, Pokémon, Twilight Sparkle, Profanity, Princess Celestia, Crossover, Human, Main 6, Thriller, Original Character, My Little Pony: Friendship is Magic
Length: 9338

When the world of Pokemon and the realm of Equestria are connected through an Ultra Wormhole, a grand adventure begins for a group of Pokemon Trainers, accompanied by Princess Twilight Sparkle.

Deep In the Kalos Region’s Santalune Forest, a lone figure enters a newly formed Ultra Wormhole, watched by several scientists. At the same time, the Elements of Harmony venture into the Everfree Forest in search of the Cutie Mark Crusaders.

These events, and the inevitable meeting of both worlds…happened six months ago. Now, after meticulous and careful planning, Princess Twilight Sparkle is allowed to travel to Kalos and begin a Pokemon Journey of her own. She is soon joined by Noah, a veteran trainer from Sinnoh with a shrouded past.

As the two of them travel together through Kalos, dark forces begin to manifest in the shadows. One seeks to conquer Equestria for their own purposes, the other strives to have the Equestrians reign over humanity.

It will take everything Twilight Sparkle has in her and more, aided by her friends in both worlds, to stop this impending conflict and restore peace to both worlds. For as far as Twilight knows in order to succeed…she must become the very best, like no one ever was.

====
Set in Generation 9 and in FIM's Season 4, will have content from both the Pokemon games and anime. Features content and characters from the fan games Pokemon Sage and Pokemon Xenoverse.
A roster of important characters can be found here.

Published 2019-09-10 20:50:01 UTC
Last updated 2024-12-23 13:14:35 UTC

Prologue - Through the Looking Glass

Equestria, Ponyville, About 7 AM

Castle of Friendship

Twilight Sparkle, the Princess of Friendship, looked herself over in the mirror for the seventh time that morning, wanting to be absolutely sure that her attire was in order and presentable.

It wasn’t a formal event she was going to, otherwise Rarity would’ve been present, and she would be wearing a gown instead of her current outfit. Currently, it was a simple shirt of light gray and a medium-length lilac skirt, a pair of tan casual-looking boots, a white jacket, and a large saddlebag, it would seem to one unfamiliar with the circumstances that she was departing on a long adventure in the countryside.

Except she wasn't going to the countryside, or anywhere known in Equestria, or the world of Equis, for that matter. She was taking a trip that was six months in waiting to the world of humanity and the mysterious creatures known as Pokemon.

Twilight still found it hard to believe at times, because for all of Equestria's recorded history, the existence of humanity had been written off as a fairytale used by scholars to explain something not known to Equestria. Yet, six months ago, the entire historical community of Equestria suffered a collective heart attack when Twilight and the Elements of Harmony entered the Everfree forest…and changed the course of history with only a single meeting.

Twilight slipped out of her room as quietly as possible in order to not wake Spike, and sat down at the kitchen table to think about what she would like for breakfast. She knew she had time to eat, as Twilight knew she was scheduled to arrive in the human world at 10AM sharp.

Despite the fact that both the human Pokemon League and the Equestrian Diarchy had assured each other, and Twilight, that if anything should happen, it would be taken care of immediately. It was quite a promise, but Twilight wasn't totally convinced just yet.

After fixing herself a plate of hay bacon, toast, and eggs, Twilight began to eat, trying to keep her mind off of the fateful meeting she had six months ago. However, her nerves led her to replay the events in her mind, as she had countless times before…

Everfree Forest, Six Months Prior

About Ten AM

"Are ya certain that those three came this way?" Applejack asked Twilight, as the six Element Bearers continued to walk along the path that led to the Castle of the Royal Sisters. "Because I swear I've told Applebloom, Sweetie Belle, and Scootaloo at least fifty times to stay out of this Celestia-forsaken forest by now."

"It wouldn't surprise me in the least if it was more like a hundred and fifty times, Applejack." Rarity added. "Those three are always cooking up some harebrained scheme to get their Cutie Marks. It's a miracle none of them have been seriously hurt."

"Well, you can't blame 'em for trying." Rainbow Dash replied, lazily hovering above them. "I've tried to talk to Scootaloo about being less reckless, but she won't listen."

"Less reckless...as compared to who?" Twilight smirked, and there was a brief round of laughter.

"Yeah, yeah…" Rainbow Dash rolled her eyes. "Seriously, though, it's strange we haven't found them by now."

"I agree." Fluttershy added, quiet as ever. "Wait…does anypony else smell that?"

Pinkie was going to ask what exactly Fluttershy had caught a whiff of, when she began to smell the sound of burning wood, and hear the crackling of logs.

"There's a fire in the Everfree?" She gasped. "I'll head back to Ponyville and get the Fire Crew!"

Just as she was about to speed off, Twilight snagged her friend with her magic and sat her down next to her, confusing the other Element Bearers.

"Just wait a second." Twilight said. "If there was a forest fire, where's all the smoke? We would've noticed it earlier if there was one."

"Yeah, and who would've set it?" Rarity added. "The Weather Ponies didn't schedule any thunderstorms for today, did they, Rainbow Dash?"

"Nope." Rainbow Dash said. "It may be summer, but we're not in storm season just yet."

"So who's out there?" Fluttershy thought out loud. Before anypony else could speak, Pinkie Pie pulled a lightbulb attached to a pull string out of her mane, zipped into the views of all that were present, and turned the lightbulb on.

"I've got it, somepony's camping out here!" Pinkie exclaimed happily, feeling as if she'd solved an impossible math equation.

"Who'd be crazy enough to camp out in the Everfree…except…" Twilight mused, and then she and the other Elements came to the same conclusion instantly.

"Applebloom, Sweetie Belle, and Scootaloo." they said not only in unison, but in a very frustrated tone.

"Let's just follow the smoke trail, it should lead us right to them." Twilight took the lead, and as the Elements did just that, they could hear the voices of the Cutie Mark Crusaders through the trees, along with another voice they didn't recognize. It was feminine, and slightly aged, but it still rang true with experience and confidence.

"Wow, miss, that's just amazing!" said Applebloom. "You think we could get our Cutie Marks in Pokemon training?"

"What exactly is Pokemon training?" Twilight asked the other Elements, who shrugged. Then, the female voice spoke again.

"While I do admire your enthusiasm, training a Pokemon requires a lot of hard work, effort, and dare I say, age and maturity. Pokemon are more than just simple creatures, they have hearts and minds of their own. It takes more than just wanting to be a Trainer to actually, truly understand the bond one can have with their partner Pokemon, and it can't be forced to happen just like "that"."

The female voice accented her final words with a snapping sound.

"Also, as I understand it, you're all still quite young." the voice added. "The Pokemon League only allows Trainers to start their journeys at the age of ten at the earliest, and that's with a regional Professor's approval. The normal age most aspiring trainers begin at is at thirteen years old."

"And even so, a Pokemon trainer often travels quite a lot across the regions of the world, and that can be quite difficult at times. From jungles, deserts, city streets, open plains…it's not an easy thing to do."

"Aww…" the three Cutie Mark Crusaders chorused in disappointment.

"Don't let me discourage you, however. You've all got potential to become a trainer at some point, but there'll need to be a lot of maturing between then and now." the voice finished. "Besides, I'm almost forty, and I still haven't seen some parts of the world I come from."

As Twilight and the other Elements pushed aside some underbrush and entered a clearing, they finally glimpsed the source of the unknown voice.

It was a tall, feminine being, wearing black robes with gold highlights and a fur lined collar, cuffs, and coattail. She had long blonde hair that cascaded down to her waist, and intelligent gray eyes.

Before Twilight and the Elements could speak, the being motioned for them to come closer.

"Oh, hello." the being said in a calm, kind voice. "I presume you're the Elements of Harmony my new friends here told me about?"

"That's us." Twilight said. "Who are you, and what are you?"

"Well, my name is Cynthia." the being replied. "I'm a human, and rest assured I'm here in peace. As a matter of fact, I'm doing a favor for a friend of mine by coming to this world."

"Wait, human?" Twilight gasped. "Humans are a myth! All the best historians and scholars in Equestria have said so over hundreds of years of research!"

"Well, they can't exactly say that anymore, now can they?" Cynthia smirked. "I can very much say with confidence that I am one hundred percent human…Would you like some of my herbal tea? You seem rather dizzy all of a sudden."

Twilight, who was in fact feeling rather dizzy, accepted a cup from the kettle that lay at a boil over a campfire, and drank. To her surprise, she felt immediately refreshed and quite perked-up with only a few sips.

"This is really good." Twilight said, as the rest of her friends sat down. "Well, I'm Princess Twilight Sparkle. This is Applejack, Rarity, Fluttershy, Pinkie Pie, and Rainbow Dash. If you don't mind, would you like to come back to Ponyville with us? It's not that far, and I'd love to hear more about the world you come from."

"Oh, that sounds wonderful." Cynthia smiled, as she extinguished the campfire. "Just give me a moment here to pack up my things."

"Let me take care of that." Twilight nodded, as she used her magic to pack up the campsite and nearly place everything into a black backpack that lay nearby in only a few seconds.

"Fascinating." Cynthia mused. "Was that the magic that your siblings here told me about?"

"Yes it was. Simple telekinesis is kind of a simple application though." Twilight said, about to slip into what was called "lecture mode", when Applejack wisely interrupted that they should get moving.

"Right, my apologies." Twilight blushed in slight embarrassment. "Shall we be off?"

"Lead the way." Cynthia replied.

As the group of ten exited the forest, and reentered the town of Ponyville, all activity came to a sudden halt at the sight of Cynthia. However, once Twilight called out that she was friendly and here in peace, the air around the residents calmed considerably.

A few of the locals waved to Cynthia, who waved back casually and kindly. One mint-green mare, however, seemed quite enamored by their visitor's hands, and was quickly shown away by another.

"This is quite a pleasant town." Cynthia noted. "Reminds me of another place I've been to back in my own world. I own a vacation home there."

"Where might that be?" Applejack asked. "If it's like Ponyville, I wouldn't mind going there myself sometime."

"It's called Undella Town, located by the eastern seaside in the Unova region." Cynthia replied. "I usually take a seaplane from my home region of Sinnoh, and I get there within a day if I plan things right."

"How many other regions are there?" Twilight asked.

"In the current Pokemon League, besides Sinnoh and Unova, there's Kanto, Johto, Hoenn, Kalos, Alola, Galar, Paldea, and now, the Urobos and Eldiw regions as well." Cynthia said, as they arrived at and entered Twilight's castle. "I can get my world map out if you'd like."

"Sounds great!" Twilight said with some glee in her voice. "Shall we get started?"

====

Twilight blinked her eyes open, and upon realizing that she had fallen asleep again, she quickly checked the grandfather clock nearby. She breathed a sigh of relief at seeing it hadn't been too long since she had woken up, and moved to clear her dishes.

As she composed herself and headed towards the castle doors, she heard steps coming from behind her.

"You're heading out, Twilight?" Spike asked.

"Yes, just about." she replied. "Hey, Spike? You know what to do if anything happens, right?"

"Yeah. I also know that the other Elements will check on me every so often, and I'll remember to feed Owlicious." the dragon replied. "Hey, Twilight…stay safe."

"I will, Spike." Twilight nodded, giving a grateful smile as she embraced her number-one assistant. "I'll see you in six months."

As she exited her castle, and Spike closed the doors behind her, she began to walk towards the train station. There, an express train would take her to Canterlot, where a new world would await her.

"Here goes." she murmured to herself as she boarded and settled down onto a couch in one of the lounge cars. "Let's see what the world of Pokemon has to offer."

The train was soon moving at a steady pace to the capital, and as Princess Celestia bid the sun to rise over Equestria, Twilight fell asleep again to the steady rumbling of the train wheels.

Author's Note

It's back and newly remastered!

Yeah, I liked this prologue a lot better than the first iterations. I hope you do too.

Chapter 1 - First Meetings

Twilight emitted an apprehensive sight as the train entered Canterlot’s Royal Train Station. Just from what she could see from inside the train, she reasoned that the Princesses, her brother, and her family had come to see her off on her journey personally.

Which was accurate, as all of the aforementioned ponies were standing on the arrivals platform, waiting for her. As she exited the train, after using her magic to fetch her sidebag, she approached her friends and family with the best smile she could muster.

“Well, Twilight, the time has come.” Celestia smiled, giving off a reassuring feeling. “I hope you’re excited to finally travel to the Kalos Region.”

“I am.” Twilight replied. “I wish I was able to say goodbye to my friends, though…”

“Hey, you’ll be able to talk with them whenever you want.” Shining Armor nodded. “Plus, Professor Sycamore already made some accommodations for you when you get there.”

“What sort of accommodations?” Twilight asked, raising an eyebrow. “I didn’t ask for anything like that when I met Professor Sycamore.”

“It was his and my idea.” Cadance replied. “When you arrive, there should be a veteran trainer waiting for you at the gate. He’ll have a placard with your name and the Equestrian Royal Seal on it, so you’ll know it’s him. Not only that, Professor Sycamore has a full set of Pokemon for you to have when you reach his laboratory.”

“Well…thanks for that. I guess it’s better to have and not need, then need and not have, right?” Twilight smiled. “I guess I should be off. I’ll be in touch as often as I can, I Pinkie-promise.”

“Are you sure about that?” Shining Armor gave a mirthful smile.

“Cross my heart, hope to fly, stick a cupcake in my eye.” Twilight laughed. After exchanging multiple hugs with her friends and family, she headed towards a building that lay next to the Canterlot Royal Palace. It may have stuck out in terms of architecture and aesthetics to any Equestrian, but for the two Princesses, it was a great leap forward.

This was the Equestrian side of the Cross-Dimensional Transfer Gate. Inside the building lay a portal to the world of Earth, a series of offices and lodgings for diplomatic personnel, and some other necessary features, such as a general store called a “Poke-Mart”, and a medical section called a “Pokemon Center”.

Twilight had already acquainted herself with Nurse Joy and her partner, a Pokemon called Audino, when she had helped supervise this building’s construction a few months earlier. Nurse Joy had also instructed Twilight in use of the Pokemon Center’s PC Storage System, and how to transfer whatever Pokemon she caught back and forth between the PC and her roster.

As Twilight approached and greeted her, Nurse Joy provided her with a wallet and 50,000 units of human currency, along with six spare Poke Balls, several Potions and aid items, and a device called a Rotom-Phone.

“The Pokemon you’ll need to activate it will be given to you when you reach Professor Sycamore’s lab in Lumiose City.” Nurse Joy said in an encouraging manner. “From all of us here, Princess, good luck and take care!”

Twilight smiled, thanked Nurse Joy, and opened the door that led to the portal’s departure station. After placing her newly-acquired items safely into her sidebag, Twilight stepped forward and onto a horizontal conveyor belt. The portal spun to life, and a white vortex appeared in front of her at the end of the belt.

Twilight closed her eyes and held tightly onto the handrails, remembering the instructions she had been given by Princess Celestia prior to this, and walked through the vortex as everything around her turned into a brilliant expanse of white light.

====

As her vision returned to normal, Twilight stepped off of the conveyor belt and into the Earth side of the Transit Gate. Wasting no time, she took off towards the exit doors, entering the main hub. She had transformed into a human-esque body, but she wasn’t surprised, as she had learned this would happen when Princess Celestia went through the portal herself.

It didn’t take too long to find the male Pokemon trainer she was supposed to meet, as he stood confidently near a cushioned bench, holding the placard with the Equestrian Royal Seal. He was a little taller than Twilight in her human form, with pale blonde hair and jade green eyes. He wore cargo trousers with hiking boots, and a white Poke Ball t-shirt over a long-sleeved gray base layer shirt. He also wore a scarf that was the same color as his eyes with a rather unique pattern, and a hiking backpack colored rust-brown. A set of Poke Balls lay clipped to his waist, along with a small green sash.

“Hello.” Twilight greeted him. “You’re the trainer that Professor Sycamore sent?”

“Yes, that would be me.” The young man replied. “I’m Noah…and you must be Princess Twilight Sparkle?”

“That's me. I prefer just Twilight, but it’s good to meet you, Noah.” Twilight replied. “Shall we be off?”

“Yep.” Noah then added, “Got anything else with you?”

“No, this is everything.” She replied. “Will you lead the way?”

“Sure. Professor Sycamore’s waiting for us out front.” Noah nodded, and they began to walk towards the front doors of the hub. Twilight’s eyes darted from area to area, taking in the sights of the building. The Poke-Mart here was far larger, and seemed to have more goods in stock compared to the one in Equestria.

Furthermore, there were other humans here, along with their Pokemon partners. Some were construction workers, but others wore suits and ties or high-visibility vests. Twilight caught a glimpse of a four-armed Pokemon wearing a wrestler’s belt that was hefting several steel girders, seemingly without any effort.

“Do you like what you see?” Noah smirked at Twilight, whose jaw had gone slack at the sight. “That’s a Machamp, the Superpower Pokemon. It’s a Fighting-Type and the final evolution of Machop. They’re bulky enough to move entire mountains, at least according to the Pokedex.”

“Those Pokemon are that strong?” Twilight flinched. "That's...hard to imagine."

"Well, that fact comes from the Pokedex, but it isn't always a reliable source of info. There's always new things being added to it, so sometimes the wires get crossed up, so to speak." Noah replied, ushering Twilight along. "Come on, Professor Sycamore's still waiting for us."

"Right!" Twilight affirmed, as she followed Noah outside and through a set of double doors. As Professor Sycamore approached with a casual wave, Twilight looked him over, not really sure of herself. She had expected a Professor of the Pokemon world to be more…uptight and scholarly-looking. To his credit, he did look the part, clothing-wise.

The Professor's lab coat was a crisp white, and he wore a navy blue buttoned up shirt with black pants and brown field loafers. Otherwise, he seemed very upbeat and exuberant.

"Ah, Princess, welcome to Kalos!" he greeted cordially as Twilight and Noah approached. "I hope everything went well?"

"Yes, thank you. It's a pleasure to meet you, Professor." Twilight returned the kindness shown to her with her voice. "Where are we heading off to now?"

"My laboratory, where we can get you a few extra things before your journey begins!" Sycamore replied, as he opened the doors to a modest-looking taxi with a pleasant smirk. As Noah and Twilight sat down in the backseat, Professor Sycamore sat up front with the driver.

As the taxi headed away from the terminal and towards the skyline of Lumiose City, a figure watched from a nearby gray limousine. He was about Professor Sycamore's height, with pepper-black hair tied back into a tail. He wore a suit and ebony necktie, which was emblazoned with a purplish-colored ringed planet and a K done in pale gold. As he settled back into his seat, he turned to a large computer monitor, where a single icon flashed white.

He touched the symbol, and wearily leaned to the side as a set of four blurred faces appeared.

"The Princess has arrived," he said in a calm manner. His voice was smooth, but there was a certain air of age and exhaustion to it. "It would seem that everything is planning out as I assumed."

"Good to hear, sir." the top-left face spoke in a brash, masculine tone. "Do you need me to move in and grab her while she's off-guard?"

"No, Derek. That would be a foolhardy and wasteful move." the man replied. "We are strong, but make no mistake. The Princess has powerful allies, an unmatched and formidable supply of magic, and I daresay…a quite exceptional Pokemon Trainer has been chosen to accompany her. I say these things with certainty."

"What makes you so sure of that?" another voice asked, this one being feminine.

"The trainer she is with is named Noah, and he hails from the Sinnoh Region. He has already made quite a name for himself. He has defeated twenty-three Gym Leaders and counting across Sinnoh, Unova, and Kalos, all in the span of four months." the man replied. "If I recall correctly, the reason he is currently in Lumiose was originally to challenge Clemont for his twenty-fourth Gym Badge."

"However…" the man continued after placing a small medicinal tablet into his mouth. "He was asked by Professor Sycamore to accompany Princess Twilight on her journey."

"Alright, then what's his battle style?" the third face asked. "The more we know, the better."

"Indeed. Noah battles with precision and level-headedness, and uses jack-of-all-trades strategy. I must give credit where it is due, his team is very well-balanced. Because of this, it is difficult to predict his next move." the man replied. Then, he coughed several times, before wiping his mouth and face with a handkerchief. Even in the dim light, the man could see a red stain on the fabric.

"Are you alright, sir?" the second voice asked. "I...don't remember you saying you were ill or anything when you recruited us."

"I have a…unique condition." the man breathed out roughly several times before his lungs settled. "The nature of which has puzzled many doctors around the known world. I am taking an experimental medicine to alleviate its symptoms. However, the general consensus I have gathered is that I cannot be cured, only treated until my inevitable passing."

"You mean, it's…terminal?" the third voice asked, sounding quite surprised.

"Yes, and I make no secret of it." the man sighed. "Enough of that, I have your orders. Derek, you are to watch the Princess and Noah from afar, but do not interact with them. Keep us updated on their movements. Stanton, you and Vanessa shall keep training the new recruits. Julian, is the prediction engine almost finished?"

"We are at seventy-eight percent completed, and climbing." Julian replied. "It will be ready when you require it.'

"Good. That will be all. Driver, back to my estate." the man said as the monitor shut off. As the limousine drove off towards the Santalune Woods, a cool wind swept through the area as clouds began to gather, signaling the coming of the rain.

Author's Note

Well, this took a while. I admit, when I published my newest chapter for Ghost Recon: Echo Solace, and when I resumed working on my Star Wars story, I remembered that this story still needed an update after so long.

So here it is. The mystery man's name will be revealed later, but if you were wondering about the specifics of his disease, he developed his condition and blames it happening on something fron Equestria.

Not to mention that he's not the only evil team leader that will be in this story. That one's still under wraps, though. I'm not telling who it might be until the big reveal.

Anyway, I hope you enjoyed this chapter.

EDIT - 12/8/2023 - Fixed a few typos, cleaned up a few excess sentences.

Chapter 2 - An Eventful Evening

"Well, Sacre Bleu!" Professor Sycamore huffed as the taxi came to a stop outside of his laboratory. "This rain shows no signs of stopping. You two should head inside, I'll handle the fare."

Noah nodded and opened the left side door, with Twilight following close behind. Twilight knew there were spare clothes for her in her bag, but she hadn't thought of bringing a jacket with her or anything for adverse weather. Noah opened the door, and she gratefully nodded to him as they entered the laboratory's main hall.

"I was expecting it to be a bit more…scientific here." she mumbled to herself, looking at the environment. "This place seems a little underwhelming."

"Well, this is just the entrance hall." Noah replied. "Professor Sycamore's lab is upstairs, and the Pokemon house is straight ahead."

"You've been here before?" Twilight asked. "Is that why you know the layout?"

"Yeah, I've been here several times in the past." Noah nodded, exhaling deeply. "Though…the last time I was here, it was more chaotic due to an emergency situation."

"What kind of emergency are we talking about?" Twilight raised an eyebrow, looking at Noah with a bit of suspicion.

"It was a Pokemon related emergency." Noah clarified. "It's a long story, and it…might not be a pleasant one to hear."

"Indeed, and a tiresome one to boot." Professor Sycamore added as he entered, his coat now darkened from the rain. Twilight was about to ask another question, but Professor Sycamore spoke first.

"You two should head upstairs to unpack. I'll get some dinner made for you both in the meantime. It's late, and I believe the storm outside won't pass until the morning, according to my Holo Caster's news feed."

Twilight and Noah nodded and proceeded down the hallway towards the guest rooms, however, Twilight was still quite curious about what kind of emergency that Noah and Professor Sycamore had mentioned.

"Hopefully it's nothing serious, and I'm getting all worked up for nothing." Twilight thought, walking towards a room on the right side of the hallway. "Though…from their voices it must've been bad, or even dangerous. I guess it's none of my business…but I do want to know."

As she laid down on a plush bed with blue sheets, she placed her bag to the side and exhaled deeply, as she began to fall asleep. Twilight tried to get back up and force herself to stay awake, but eventually, she gave up and pulled the covers over herself. In only a few minutes, she was sound asleep.

====

As Noah entered the lab's kitchenette, Professor Sycamore motioned for him to sit down. The Professor had managed to whip up a dish of warm rice, berry juice, and a serving of barbecued ribs. Noah thanked the Professor, and dove into his meal.

"Slow down, Noah." Sycamore admonished, eating his ribs at a more refined, slower speed. 'I don't want you to choke on something."

Noah gave a grunt of acknowledgement, and slowed down accordingly to match the Professor's pace. Eventually, he stopped and looked back towards the hallway that led to the guest rooms.

"Twilight's missing out on dinner…I hope she's alright…" he mused, with a worried tint in his voice.

"I'd imagine she's resting at the moment." Professor Sycamore replied. "Traveling from Equestria all the way to Kalos would likely put quite a strain on her body and mind. Besides, I can leave some things out for her if she's hungry later."

"That is true." Noah nodded. "I'll help clean up once we're done, if you need my help."

"I'd appreciate that Noah, thank you." The professor nodded and stretched his arms outward before standing up. "Come on, let's get started. These dishes can't do themselves, you know."

"Oh, I'm aware of that." Noah smirked, heading over to the washing machine and sink. "You know, thinking back to that…situation a few months ago really made me think about how much Pokemon rely on us, and us on them. If I hadn't found that crate at Lake Valor in time…those Pokemon would've been…"

"I know, Noah." Sycamore replied. "It was fortunate on our part that we recovered them, and were able to reunite them with their trainers or partners. It certainly was touch and go for quite some time."

There was silence between them for a few minutes, before Noah took out a Poke' Ball from his bag, staring at one specific point. On the topside, at about forty-five degrees, a jagged white line could be seen. It didn't interfere with the Poke' Ball's functionality, and it easily could've been sealed up, but for Noah, it was a memento of the past for the Pokemon within.

He sighed, placed the ball back in his bag, and resumed washing the remaining dishes in silence with Professor Sycamore.

====

Twilight blinked her eyes, slowly waking up to an unfamiliar room. She was wary at first, but then she remembered where she was and why she was there. She leaned backwards to look at the electronic clock on the nightstand.

"It's almost eight…" she huffed out loud. "Did I really sleep that long?"

"You did, but it's fine." Noah said, placing a full plate of food on the nightstand. "We saved you a plate, and it's still warm. I know Equestrians don't eat meat, so I put the ribs away for you."

"Thanks." Twilight nodded gratefully, beginning to eat, and it didn't take her long to clear her plate. She cleared her throat, causing Noah to glance at her in a curious manner.

"I didn't mean to intrude earlier about the emergency you mentioned." she said quietly. "It wasn't my place to ask about it."

"It's okay." Noah replied. "Would you like to know the full story? It's okay if you don't."

Twilight nodded in response.

"Well, here goes." Noah sighed. "This was about three months ago in the Sinnoh region, near Lake Valor. I was hiking along the lakeshore when I noticed a storage crate just sitting there, and judging from the condition it was in…it had been underwater for a good amount of time. Sitting next to it in the mud was a damaged Pokeball."

"I opened the crate, and found more Pokeballs on a six-by-six rack, four racks deep." he continued. "I called Officer Jenny on the spot, and she was there in a few minutes, along with Nurse Joy."

"The thing is, once we got the crate and all the Pokeballs back to the Pokemon Center, Officer Jenny found a symbol printed on the crate that made her call for backup, right then and there. It was the insignia of a woman called Pokemon Hunter J."

"A Pokemon…Hunter?" Twilight asked, not sure if she would like the answer.

"A person who steals Pokemon, either from the wild or from trainers, to sell on the black market." Noah replied, making Twilight's jaw drop. "Pokemon Hunter J was regarded as the best of them all."

"She sounds really evil." Twilight replied. "I hope she gets caught sometime."

"That's the thing, Twilight." Noah sighed. "She's dead."

Twilight's train of thought came to a screeching stop as she pondered what Noah had just said.

"She's dead? Then who killed her?" she murmured, feeling quite horrified.

"I'll get to that." Noah nodded. "A few months before that, Hunter J was in deep with a criminal group called Team Galactic. Their leader, Cyrus, wanted to create a new world in his image, and to do that, he needed the powers of the Legendary Pokemon Dialga and Palkia, who control time and space. In order to get that power, he needed the Pokemon called the Lake trio, consisting of Mesprit, Uxie, and Azelf."

"Team Galactic soon captured Uxie and Mesprit, but before that, those two Pokemon used a powerful move called Future Sight. That move essentially creates a powerful storm of psychic energy to strike the target at a later time, so keep that in mind."

"Once Pokemon Hunter J departed in her airship, after being paid by Team Galactic for her efforts in capturing Mesprit and Azelf…the Future Sight attack hit J's airship dead on. It began to fall into Lake Valor, where a massive vortex awaited it. Once it hit the wall of water and began to sink deeper into the lake…the airship's engines went critical and it soon exploded."

"The only trace of J that was recovered was her tracking headset." Noah continued. "She and her crew were never seen again, but there were still plenty of Pokemon who were lost when the ship went down…or so we assumed."

"So some of the Pokemon on board survived?" Twilight asked.

"Yeah, once Cyrus was defeated and the Lake Trio were freed, they allowed us to send salvage divers down to the wreck. They were able to extract a bunch of the crew's Pokemon that were in their Poke Balls, and a good amount of other Pokemon that had been turned into statues. We assumed that was the end of it…until I found that crate." Noah replied.

"As it would turn out, the Poke Balls in that crate contained more stolen Pokemon that we were able to send back to their trainers safely. The one thing that caused the emergency was the damaged Poke Ball I found."

"There was still a Pokemon in it, but we couldn't know what it was unless we got it out of the Poke Ball. Which was tough to do given its damaged state. A Poke Ball maker named Kurt came down from Johto to help, and we barely managed to transfer the Pokemon out to a new Poke Ball."

Noah sighed deeply, before continuing in a more quiet manner.

"Inside that Poke Ball was Pokemon Hunter J's partner, Salamence." he said. "It took us a week to get him back to physically full health, but his mental state was something else. Salamence was distraught over losing the only partner he had ever known, and it was really hard for him to adjust to being without her."

"He would lash out in sadness towards anyone that approached him, and he isolated himself from other Pokemon. It was looking bad for a while, until I volunteered to take him with me and become his new partner." Noah sighed, remembering the troubles that followed. "For a while, Salamence wouldn't listen to me, and even then, it was hard to get him out of his Poke Ball in the first place."

"Three weeks afterward, Salamence and I got through to each other, and he's been my best partner ever since. He outgrew his old vicious temperament that J had forced into him, and he's a lot better now…but he doesn't really trust anyone apart from me."

"I'm so sorry to hear that." Twilight said quietly. "At least he's found a new partner in you. That must mean something to him."

"Yeah, it does." Noah replied, standing up and stretching. "Hey, we should rest. Tomorrow's another big day. I'm sorry I had to ramble on like that."

"It's just fine with me. Goodnight, Noah." Twilight smiled, and as Noah left the room, she laid back down to sleep as the rain began to ease up outside, signaling the storm was passing by.

Author's Note

An update at long last. Sorry this took so long.

Chapter 3 - The World Champion's Visit

Feeling the warmth of the predawn sunlight was the first thing that roused Twilight Sparkle from her slumber. At first, she was taken a bit off-guard by her unfamiliar surroundings, but her mind soon settled once she remembered where she was.

”Good morning.”

Twilight turned to see Noah was standing in the doorway, already dressed and ready for the day. The Princess, with her ruffled hair and still-sleepy expression, looked like she had just tumbled down a mountain.

“Morning.” Twilight replied in a quiet voice, using some magic to straighten out her hair. “What’s on the agenda for today?”

“Not too much. Though, Professor Sycamore’s meeting with two other professors later in the day, and your team of Pokemon from the Pokemon League should arrive by dusk.” Noah nodded. “I guess that I'll leave you be so you can change.”

Noah promptly closed the door, and Twilight quickly located her bag and suitcase, which lay on the far side of the room. After quickly picking out her usual choice of attire, she stepped onto the tile floor of the bathroom to freshen up.

After taking a shower, she vigorously brushed her hair and washed her face with some moisturizer. Once she was finished, Twilight looked at herself in the mirror and gave a nod of approval.

”My first full day in the world of Pokemon.” she said to herself. “Let’s make it a good one!”

As she stowed her toiletries in her bag, Twilight did have to admit that her bag had a great carrying capacity. There were pockets and pouches for every sort of thing you could fit inside. Some even had labels pre-patched into them.

"That's neat, they really thought of everything!" Twilight cheered. "Alright, let's go!"

====

“Ah, you’re just in time for breakfast, Princess!” Professor Sycamore greeted her from the dining table. “Was everything comfortable?“

“Yes, it was, thank you.” Twilight nodded as she sat down. “I heard you’re meeting with two other professors today.”

“Indeed I am.” Sycamore replied. “Professors Mangrove and Aster, to be exact. They’re the resident professors of the Urobos and Eldiw regions, and both came a long way. I also believe they’d be thrilled to meet you, Princess.”

“Really?“ Twilight replied, a bit surprised as she had never heard of Eldiw or Urobos before now. “Back in Equestria, Cynthia only told me about the Kanto region through the Paldea region.”

“That’s because their introduction into the Global Pokemon League was put on hold when we made contact with Equestria.” Sycamore replied. “Now that it’s been six months, we can get back to business regarding them.”

“That’s good to know.” Noah said as he entered the dining room, carrying his breakfast on a clean porcelain plate. “I wonder what Pokemon they have in those regions…I’d imagine they’ve got some we’ve never seen or heard of before.”

“That's correct, Noah." Also, Pokemon from Eldiw have some unique features as well. For example, they have Pokemon belonging to the Sound-type. Here in Kalos, Noivern is a Dragon and Flying type, but in Eldw, it’s a Dragon and Sound Type. There’s plenty of Pokemon that follow that example as well. I’ll have to ask Professor Aster about getting a full list of them…” Professor Sycamore replied. “Anyway, our food’s getting cold, so dig in!”

At hearing this, Twilight and Noah proceeded to do just that, and their plates were emptied in no time.

About a half hour later, as Noah and Twilight strolled through the busy streets of Lumiose City, Twilight was caught off guard when Noah suddenly stopped walking and began to stare at a pair of humans, a boy and a girl, watching a video appear on a large screen mounted on a building nearby. A yellow, mouse-like Pokemon with a tail shaped like a lightning bolt was perched on the boy’s shoulder.

“Noah?” Twilight asked, confused at the sudden stop and her friend’s awestruck expression. “Is something wrong?”

Noah didn’t respond as he continued to keep his gaze centered on the two of them, as he took a few tentative steps forward.

“There’s no way that's him…” he murmured. “This is my chance! I can finally…”

“Noah, what’s going on here?” Twilight asked in a louder voice, snapping Noah back to reality. “Is everything okay?

“Yeah, everything’s great!” Noah replied in an excited manner, awkwardly rubbing the back of his head. “Sorry, I just can’t believe I’d see him in public so soon!”

“Who exactly are you talking about?” Twilight was visibly confused, not knowing why Noah was so pumped up all of a sudden. She turned to glance at the two humans, who were now deep in conversation.

”Twilight, if I’m not mistaken, that male trainer over there is Ash Ketchum, and his partner, Pikachu.” Noah replied. “He's the current Pokemon World Champion!”

Twilight’s eyes significantly widened as she processed Noah’s words, especially the “World Champion” part. From Noah's tione of voice, he was thoroughly hyped up.

“At the World Masters Tournament a while ago, he beat multiple region Champions, including Steven Stone, Cynthia, and Leon.” Noah continued speaking. “He’s considered the strongest ranked Trainer in the world! I never thought I’d get to see him like this until now.”

“Well, go introduce yourself.” Twilight suggested. “What’s stopping you?”

“I’m going to, right now I want to savor the moment.” Noah replied sheepishly, turning to face Twilight. "It's not every day you get an opportunity like this."

Twilight raised an eyebrow, and wanted to speak, but she heard footsteps approaching, and the two of them turned to see the the couple had noticed them, and was walking over in a relaxed yet curious manner.

“Hey, you’re Noah, right? From the Sinnoh Region?”

Noah’s jaw dropped slightly as Ash and Pikachu stepped forward, followed by a girl with shoulder-length honey blonde hair and blue eyes. She wore a gray sleeveless cardigan, with a red and white skirt and gray boots. On the other hand, Ash wore a black shirt with a Poke Ball logo, pale blue jeans, and a gray long-sleeved jacket, with a gray duffel bag.

“Yeah, that’s me.” Noah replied. “And…you’re Ash Ketchum.”

“The one and only. I've been following your Gym challenge." Ash replied with a smile, offering a handshake, which Noah accepted. “This is my partner, Pikachu, and my girlfriend, Serena.”

Serena gave a friendly wave, and Twilight gave a smile in response before she breathed in and introduced herself. Serena then perked up like she just remembered something important at hearing Twilight's name and title.

“I believe Ash and I heard about you from Cynthia, Princess Twilight. I didn’t think I’d get to meet you face to face though, Princess! Or, your Highness…what exactly should I call you here?” Serena asked.

“Just Twilight is fine, thank you.” Twilight responded. “Noah and I were just walking around when he recognized you, Ash. I didn’t think I’d meet this world’s strongest trainer so soon.”

“Well, I may a strong trainer, and the current World Champion, but I’m not a Pokemon Master just yet.” Ash said, his Pikachu giving a cry of approval. “That’s what I want to be more than anything.”

“A Pokemon Master?” Twilight asked. “What exactly does that mean?”

It means I want to be friends with all the Pokemon out there, and experience everything that goes with it.” Ash said, with an almost soft yet proud voice.”I set out with Pikachu all those years ago back in Kanto, aiming to be a Pokemon Master, and I like to think that there’s still a long road ahead of us until I reach that goal.”

"Woah." Twilight said, sufficiently awed at Ash's outlook. There was a few moments of silence, before Ash noticed a few passersby were staring and whispering at them.

”Well, anyway, Ash and I were going to surprise Professor Sycamore at his lab before we head back to our hotel.” Serena chimed in. “Would you like to come along?”

“Sure.” Noah replied. “Let’ get moving!!”

As the four of them began to head back towards Professor Sycamore’s laboratory, Twilight took in a breath and composed herself. She had wanted to see more of Lumiose, but it seemed Noah was really enjoying being in Ash and Serena’s company. He seemed more open and even happier, which was a contrast from the direct and to-the-point attitude that he had when they met at the Transfer Gate.

It was strange seeing Noah like this, Twilight mused, sensing there was something else behind the shift in his mood.

“Hey, Twilight, are you coming?”

Realizing that the group was waiting for her, she quickly called back that she was fine and quickly walked to catch up with Ash, Serena, and Noah. However, a good distance away, a larger man wearing a duster coat and trousers took a small drone out of his pocket. He tossed it into the air, and it immediately began to hover in place.

The man tapped a few buttons on his wristwatch, and the drone flew off towards the four trainers, keeping itself at the perfect distance to remain undetected. The man nodded in approval, and took out a cell phone. Tapping a number on the speed-dial, it didn’t take long for the person on the other end of the line to pick up.

”Derek.” An elderly male voice spoke. “Do you have an update for me?

“Yes, Boss. The drone’s up, and it’s tracking the target as we speak. Are you getting the feed on your end?” Derek asked.

”Yes, clear as can be.” the other voice replied. “Your reputation is holding up splendidly, bounty hunter. When I asked for the best in covert retrievals, I am glad it was you who responded.”

“Well, thanks.” Derek replied. “When should I move on the target? I take it time is of the essence, based on your health.”

“Time is of no concern.” The voice chided. “Make sure there are no mistakes made, and expect the unexpected. Equestrians are dangerous, even more so when you throw Magic into the mix. I want the target unharmed as well. Can you manage that?”

“Yep. Not a problem.”

“Good. Keep me updated on her movements in the meantime. I leave the rest to you, bounty hunter.”

As Derek ended the call, he gave a quiet huff before vanishing into the dark alley behind him.

Author's Note

Update!
EDIT - 10/10/2024 - Reworked a few short sentences, changed up a few things, will have next chapter soon.

Chapter 4 - Everything Unexpected, Part One

As the four trainers continued their walk back to Sycamore’s Lab, Twilight was beginning to feel like a third wheel. Noah was deep in conversation with Ash and Serena, and there didn’t seem to be any signs of them stopping. Despite this, she was enjoying being alone with her thoughts, and how excited she was to finally be receiving her team of Pokemon.

”Hey, Twilight?” Ash said, snapping Twilight out of her reverie.

“Ah, yes, what is it?” she stumbled over her words for a few moments, before she composed herself.

“I was wondering what Equestria’s like.” Ash responded. “Can you fill me in? Cynthia told us about a few things, but I was hoping to get a sense of the bigger picture.”

“Certainly!” Twilight said, eager to not only be included at last, but also to enter her “lecture mode”, as Spike called it. “Well, where should I start? I suppose I could begin with the three Pony tribes…Many, many years ago, even before Princess Celestia and Princess Luna’s time, there were three tribes of ponies present in the world. The Earth Ponies supplied the primary amount of food for all three tribes, in exchange for protection by the Pegasi, and for the Unicorns to bring forth day and night.”

“So, the sun and moon don’t rise and set on their own in Equestria?” Serena asked. ”Why is that?”

“That’s a tricky question, Serena.” Twilight replied. “Even before the pony tribes existed, there was a great magical event known as the Rupture. We know that this even caused the sun and moon to stand still, but it also paved the way for the existence and use of magic as a whole. There are few records that survived the passage of time that reference it, and fewer still are even legible enough to read.”

“That makes sense.” Noah murmured. “but that doesn’t answer the questio of how Equestria was formed, Twilight.”

“I’m getting to that.” Twilight replied. “When the harvests began to fail as winter set in, the three tribes became desperate to secure whatever resources they could. That led to hoarding, then more shortages, and eventually, the combined agreement to find a new home.”

”So, the three leaders of each Tribe, Princess Platinum, Chancellor Puddinghead, and Commander Hurricane, along with their aides, set out to find a new land to settle. Once they arrived in what is now Equestria, their continued conflicts led to the arrival of the wendigoes.”

“Wendigoes?” Serena asked.

”Wendigoes are creatures of ice that feed on negative emotions, such as anger and hatred.” Twilight replied. “They spread winter-like conditions wherever they go, and as the tribe leaders continued to argue over which tribe would rule the land, they were sealed in a cave by frost and ice.”

“Luckily, the tribe leaders’ seconds, Clover the Clever, Private Pansy, and Smart Cookie, were able to reconcile in time to save the land, and their leaders. Equestria was formally created shortly after that. Then, Princess Celestia and Princess Luna took over the duty of raising the sun and moon each day and night.”

Twilight was about to continue into the legend of Nightmare Moon, when she was shoved to the side by Noah. Before she could scold him, Twilight saw a long, metal arm with a claw on the end lash outwards and snatch Pikachu from Ash’s shoulder.

“Pikachu!” Ash yelped, grabbing onto the arm with both hands, his grip tightening as his knuckles turned white. ‘Hang on, buddy! I’ll get you out of there!”

“What’s going on!?” Twilight gasped, rushing over to assist Ash. “Who’s doing this?”

“I’m glad you asked!” A woman’s voice barked out, sharp and authoritative. “Now’s the proper time to introduce ourselves once again, twerps!”

“Twerps?” Noah muttered to himself, readying a Poke Ball, only for a high-pitched grinding noise to sound through the area, and Noah’s Poke Balls, along with Ash and Serena’s, to fly out of their bags and towards a large hot-air balloon, styled in the image of a cat-like Pokemon.

“Who do you think you are?” Twilight yelled. Then, three figures, two humans and a Pokemon that matched the look of the balloon jumped up, with the Pokemon holding a control board of some kind. The other two, a woman with sharp pinkish red hair done in a long curved tail, and a man with neck-length, wavy blue hair, both wearing white clothing styled with a red "R",began to chant as one.

Prepare for trouble!
And make it double!

To protect the world from devastation!
To unite all peoples within our nation!

To denounce the evils of truth and love!

To extend our reach to the stars above!

Jessie!
James!

Team Rocket blasts off at the speed of light!
Surrender now, or prepare to fight!

Meowth!
That's right!

As they finished, Ash gritted his teeth and yanked at the claw keeping Pikachu hostage with more vigor.

”I should’ve known…It’s Team Rocket!” he scowled. "I thought you guys retired!"

"Well, after getting a fresh outlook on life, and receiving a new mission from the Boss, we're officially back in business, and getting that Pikachu is first priority!" Jessie proclaimed.

"You thought you'd seen the last of us, didn't you?" Meowth taunted. "Guess the table's turned, twerps!"

"And not a moment too soon!" James laughed, placing the stolen Poke Balls into a bag. "What a fine catch for us!"

"Give those back…" Twilight yelled, stepping forward, her hands beginning to glow with magical energy. "Or else!"

"Or else, what?" Jessie cackled, only to abruptly stop at seeing a lavender aura begin to form around Twilight, growing in power with each passing moment.

"Or you're going to find out what happens when you make the Princess of Magic angry." Twilight replied, raising her right hand as more magical power formed around it.

"Hit us with your best shot!" Meowth stuck his head forward in a teasing manner. As the three criminals continued to laugh, Twilight smirked, a plan forming in her head at lightning speed.

"I plan to!" Twilight roared, summoning a magical wave in the air, and with a flick of her hand, the wave sliced through the arm holding Pikachu like a hot knife through butter. Team Rocket's laughter died out in an instant as they witnessed it happen.

"Um…I think we made her angry…" Meowth said, now feeling quite frightened.

"You think?" Jessie yelped in annoyance. "Get us out of here!"

"What do you think I'm trying to do!?" James shot back, furiously working the balloon's controls. As it began to move away, Twilight raised her left hand, and grasped the balloon in her magic, before yanking her hand downwards. The balloon smashed into the ground accordingly, and before James even raised a hand to grab the bag of stolen Poke Balls, it was gone in a flash of light.

Twilight caught the bag as it reappeared in her arms, and Ash, Serena, and Noah quickly retrieved their respective Poke Balls. Pikachu then dove in front of Twilight, electricity crackling from his cheeks.

"Well, that's something you don't see every day." James said flatly, only to jump to his feet alongside Jessie and Meowth. "But that won't stop us!"

The two human members of Team Rocket then each threw six Poke Balls of their own, and out came Jessie's Seviper, Yanmega, Wobuffet, and Gourgeist, alongside her Swoobat and Jellicent, both of which had evolved during their time away.

In a similar manner, James released his Amoongus, Morpeko, Carnivine, and Mime Jr, but just like Jessie, his Yamask and Inkay had evolved into Cofagrigus and Malamar.

"Looks like they've shaped up their teams, and even evolved some of their Pokemon as well." Ash said in a low voice. "Pikachu, let's go!"

"Delphox, help out!" Serena added, as her partner was released from its Poke Ball. Noah also sent out his Salamence, and as all the Pokemon involved took up battle stances, Twilight lowered her eyebrows.

"Three of our Pokemon against twelve of theirs." she mused. "If only I had Pokemon of my own, I could help…but maybe…I don't need a Pokemon to be useful right now!"

"Looks like you're outnumbered!" Jessie called. "Seviper, Poison Tail! Yanmega, Bug Buzz!"

"Cofagrigus, Shadow Ball! Morpeko, Dark Pulse!" James added, and as the four Pokemon let loose their attacks, Pikachu, Delphox, and Salamence braced themselves against the incoming moves…only for them to impact against a lavender colored shield of light.

Ash, Serena, and Noah turned to see Twilight's magical aura had returned in full force, and she then fired off a powerful beam of magical energy towards Team Rocket. With one powerful blast, all four Pokemon that had led the attack were knocked out in an instant, reducing Team Rocket's force from twelve to eight.

"That ought to even the odds." Twilight said, stepping forward. "Everyone, let me handle this. If I need help, I'll let you know."

The other three trainers looked astounded, but they followed Twilight's words and stepped back, their Pokemon going with them.

"Okay, let's go!" Twilight yelled, sending out a rapid flurry of energy blasts. As Team Rocket's eight remaining Pokemon began to charge, readying attacks of their own, Twilight braced herself for whatever would come next.

Author's Note

So, yeah. I decided to give Team Rocket a bit of a buff in this story. I feel that since they resumed working for Team Rocket after their separation, I like to think they spent some time training and working hard to be able to compete with Ash's team.

Anyway, I'm sorry it took so long to get an update out in general. I hope you enjoyed this chapter.

Next time - Two new trainers inervene in Twilight's battle against Team Rocket, and Twilight receives not one, but six Pokemon form Professor Sycamore at long last.