A/N: Hey there everyone! This is my first fanfic which I hope to continue over the next few months. Hope you enjoy it. =)

This story is set in an alternate timeline in which Latios survives the events of Pokémon Heroes. It takes place a year and four months after the events of Pokémon Heroes.

Disclaimer: I don't own Pokémon or any of its characters. Claiming to do so would be akin to using a Rattata to take on Arceus: completely and utterly ridiculous as well as suicidal.


Scarred

by csigamer1990

Chapter 1

Reports and Plots

"The infectiousness of crime is like that of the plague" - Napolean Bonaparte


The sun was setting over the suburban landscape that was Viridian City. The picturesque town had an aura of serenity and peace about it; the warm glow of twilight seemed to heighten that feeling.

However, that feeling was lost upon one man in particular. For him, he could care less about the view he was currently observing from the balcony outside his office. He had far more pressing matters on his mind; he couldn't allow anything to distract him from them.

He was dressed in a manner that signified extreme wealth and power, with a black tweed button-down suit with a white undershirt and a red tie with a checkered pattern. There was a red handkerchief sticking out of his breast pocket. He wore black dress pants and sported black wing-tip shoes. His black hair was slicked back on his head and his face seemed to hold a permanent scowl on his features. This man's name was Giovanni, and he was the leader of the Viridian City gym. However, that was only one of the titles that he held, the one that most people knew him by.

What most people did not know was that Giovanni was also the leader of Team Rocket, a major criminal organization with bases established all around the world. Team Rocket were a group whose main source of profit were in the capturing and selling of rare and exotic Pokémon for exorbitant sums of money. Although this was their current goal, it was only to further the progress to their ultimate goal: complete and utter world domination.

They worked to achieve this goal by any means necessary, from espionage and burglary to even murder. They were even known to fund and conduct cruel research programs on Pokémon in order to find ways to unleash a Pokémon's full destructive power so they, in turn, could use it to accomplish their own nefarious purposes.

While they were most prominently featured in the Kanto and Johto regions, there were rumors that Team Rocket's influence had spread to many others such as Hoenn, Sinnoh, and even Unova.

There was even talk of a small chapter being established in the desert region of Orre, although this was met with some skepticism. "Why would a major criminal organization such as Team Rocket bother to establish a base in a wasteland such as Orre?" some would say.

Their skepticism was well founded. The Orre region was mostly barren desert, with a few settlements located here and there. It was an arid environment, mostly devoid of life and easy to get lost in. And once you got lost in the desert, there was little chance that you would make it to your destination alive, as temperatures during the day could skyrocket to over 110 degrees Fahrenheit. The nights were no better, with temps dropping to well below freezing.

And then there were the sandstorms. Impossible to predict and just as hard to hide from, the sandstorms of Orre could grow humongous in size. Needless to say, you did not want to get caught in one of them, unless you wanted to spend the next month coughing dust out of your lungs.

This hostile environment translated to little to no ability to support life. Wild Pokémon were rare, and the few that did appear were those that favored the arid environment, such as Cacnea, Flygon, and Sandshrew.

Although these were viable points, it didn't serve to dispel the rumors of a Team Rocket base in the Orre region. Maybe they wanted to keep an eye on that other team down there, Team Cipher, to make sure that they didn't bite off more than they could chew? Maybe they were drawn by talk of legendary Pokémon being sighted in the area? Or maybe it was simply the fact that since Team Rocket had their hooks into every other region, why not have a base in Orre?

Whatever the reason, it was clear that Giovanni was a man of power, one who was feared by his enemies as well as his subordinates.

He continued to watch the sun set for a while, and then turned away, heading through the open sliding-glass door back into his office. He didn't bother to close it; it was a rather warm day outside and he appreciated the breeze coming through the open door.

His office was atypical for one of his stature, very spacious with some assorted fineries dotted around the room: potted plants in the corners, some paintings adorning the walls, all done by big-name artists, and a liquor cabinet behind his desk stocked with some of the best alcoholic beverages from around the world.

His desk was very neatly organized, the papers he read to keep track of various legal activities all either in a bin marked "In" for those he hadn't read yet, or "Out" for those he was finished with. The papers that kept track of his more illegal activities he kept in a compartment under his desk that only he knew about. You could never be too careful, he thought, what with the damned police snooping around, sending in moles to infiltrate the organization. They still hadn't managed to trace the activities to him though, so he made sure that his identity remained a secret to everyone but his top ranking executives, to everyone else in the organization he was simply referred to as "The Boss".

He also never signed any letters he used when communicating with members of the organization with his full name, opting instead for just using the letter "G."

Also among the things on his desk were a lamp, an intercom, a small fan, a computer, and a glass of whiskey with ice in it, which he took a sip from now, still thinking of the day's events.

His prized Persian was currently lounging in its bed at the side of his desk. It now proceeded to get up and walked over to his Master, nuzzling him affectionately. Giovanni, distracted from his musings, allowed himself a small smile as he petted the cat Pokémon's head. The Persian purred in contentment, leaning into the contact, enjoying it immensely.

Giovanni admitted to himself that his Persian was one of the few things in his life that brought him happiness, the others being money, his power as the boss of Team Rocket, and the occasional Gym Battle, the ones that actually proved challenging. True, he had many other Pokémon in his possession, all of them extremely powerful and loyal, but none of them seemed to bring him the same amount of happiness that his Persian brought him.

Just then, there was a buzz from the intercom. Setting his drink down, Giovanni pressed the button that worked the intercom.

"Yes, what is it?" he asked in a slightly irritated voice.

"Mister Giovanni, I'm sorry to disturb you, but two women by the names of Annie and Oakley are here to see you. They say they have important matters to discuss that require your attention." his secretary answered.

Giovanni was taken aback by this; he had received word that Agents Annie and Oakley had been captured during the last mission he had sent them on, to head to the island city of Alto Mare and find out what they could about something called the 'Soul Dew', a magnificent jewel of extraordinary beauty and power, said to contain the soul of a Latios, a legendary Pokémon. They were then tasked with tracking down the Soul Dew and to retrieve it to bring it back to Rocket HQ where its power could be studied, as well as to keep an eye out for the guardians of the Soul Dew, Latios and Latias, and to capture them if possible. However, they had lost contact with Agents Annie and Oakley a few days into the mission, and it was presumed they had been captured. But it now seemed like they had escaped.

"Mister Giovanni? Should I let them in?" his secretary said over the intercom, bringing Giovanni back to his senses.

"I see. Very well, let them in" he said. 'Perhaps now I'll get some answers' he thought.

"Right away, Mister Giovanni." said the secretary.

The door to Giovanni's office opened, and his secretary showed two women in before closing the door. One of them had her blonde hair in a twin bun formation and the other had blue hair styled to the sides. Both were wearing black tank tops with black leather pants and high heel shoes.

Giovanni motioned toward two leather chairs in front of his desk. "Please, sit down." Annie and Oakley graciously accepted his offer and sat down in the chairs.

"Well, ladies, while I am pleased to see you back, I am curious as to the circumstances that led you here. The last I heard, you two had been captured during the last mission I sent you on and were incarcerated. I'd appreciate it if you filled in the blanks for me." A sudden thought came to Giovanni's mind that filled him with dread. 'Perhaps they've been released to spy on me!'

"Well, you were correct in guessing that we were captured, sir. Me and my sister were indeed in prison for the last few months." said Annie.

"And let me tell you, it is not an experience I or my sister wants to repeat." Oakley said with a look of disgust on her face. The small cell, the uncomfortable beds, the horrible food, and the perverted guards were all bad enough. And then there were the lesbians. Just thinking about it sent a shiver down Oakley's spine. She wondered if she'd ever be able to take a shower again without looking over her shoulder. She was grateful that Anny was there to protect her, and she was sure Annie felt the same.

Annie nodded her head before continuing. "Indeed. Oakley and I realized that we couldn't stay there, so it wasn't long that we started making plans to escape. I won't go into the exact details, but let's just say that the prison guards were not the sharpest tools in the shed" she said with a smile.

"Not to mention we were significantly more skilled in unarmed combat than they were" Oakley said with a chuckle.

"After we'd obtained the guard's keys, it was a simple matter of sneaking our way out. We made our way to the roof, where there were some conveniently place power lines that led over the prison wall. We shimmied across and made good our escape." Annie said. She herself was so glad to get out of that drab orange prison jumpsuit, which did not suit her sense of fashion one bit.

"And just to put your mind at ease sir, if you want to confirm our story, I'm sure our escape has made headline news by now." Oakley said with a grin.

Giovanni chuckled at this "I don't doubt it will be." he said. "But there will be time for that later. I guess I should commend you for your daring escape, something even I could not have expected. But then again, I don't see how two of Team Rocket's best field operatives could remain incarcerated for long, so congratulations to both of you."

Annie and Oakley blushed a little at the praise, which coming from the Boss meant a lot. "Thank you, sir!" they both chorused.

"But, there still remains the subject of your failure to discuss." he said, his voice becoming very serious. Annie and Oakley smiles vanished abruptly and they both gulped nervously. Giovanni continued "As I'm sure you both know, this organization does not tolerate failure lightly. I find it very difficult to believe that two of this organization's best field operatives and spies managed to fail in a simple reconnaissance and retrieval mission. I hope you two have a very good explanation for this."

Annie decided to take the initiative in explaining. "Giovanni, sir, let me assure you that I and my sister undertook that mission with the utmost seriousness and that we did everything in our power to accomplish the goal you set us. However, there were a few…circumstances…" at this she cast a sharp glare over at her sister, who looked away ashamedly, "that we didn't foresee or were prepared for. If you will hear us out, we'll explain to you what happened. Should I start at the beginning?"

Giovanni leaned back in his chair, his hands clasped together. "Please do."

"Very well, sir." She paused a while to regain her composure before beginning. "As per your orders, Oakley and I proceeded to Alto Mare. We figured that the best place to start searching for info on the Soul Dew and the guardians, Latios and Latias, was to head to the city library. We snuck in at night so as not to attract attention to ourselves and searched the library for anything relating to our target. We eventually came across an old book which contained details on the formation of Alto Mare and the origin of the Soul Dew, as well as some info on Latios and Latias. It also contained instructions on how to operate something called the Defense Mechanism of Alto Mare. We'll go into more detail on that later."

"We left before we could discovered by security, taking the book with us, as we figured it might come in handy, and proceeded to Alto Mare so we could begin phase two: locate the Soul Dew and retrieve it and also to subdue and capture Latios and Latias."

"Unfortunately, this proved to be a difficult task, as Alto Mare is a very large city with many inhabitants. Also, from info provided by the book, we found out that the Soul Dew was hidden in a secret location with illusions placed around it to protect it from prying eyes, its location only known to its guardians and their caretakers."

"As if that weren't enough of a problem, the book also informed us that Latios and Latias, in addition to being powerful Pokémon of Dragon and Psychic typing, were also capable of shape-shifting into a human form as well as having the annoying ability to turn invisible, making our job that much harder."

"Fortunately, we came prepared for such a snag. Using the Devon Scope devices you provided us, we were finally able to track down one of the Eon twins in human disguise along one of the city's waterways. It had taken the form of a girl, so we assumed that it was Latias, the female twin. We must've spooked it, because it immediately started running away once it caught sight of us. My sister and I released our Pokémon, Ariados and Espeon, to give chase."

"Things seemed to be going well, as Ariados and Espeon caught up with her after a while and had managed to subdue her. But then, all of a sudden, we were interrupted by this punk Trainer and his Pikachu. When he saw our Pokémon restraining Latias (although he probably thought it was just some girl), he ordered us to let her go. We didn't take him seriously, which quickly backfired on us. His Pikachu was able to subdue both of our Pokémon all by itself! Needless to say, we were shocked. Literally as well as mentally, I might add."

'And goddamn if that Pikachu's Thunderbolt didn't hurt like hell' Annie mused to herself. 'And I paid $500 for that outfit too…' she thought angrily, recalling the outfit that was ruined as a result of falling into the waterway by way of the Pikachu's Thunderbolt.

"Anyway, this kid's interference allowed him to escape with Latias. Although we sent our Pokémon after them, they still managed to slip through our fingers." she continued, a trace of anger apparent in her voice.

"And who exactly was this Trainer that was able two of my best operatives such difficulty?" asked an amused Giovanni, a smile at the corner of his mouth.

"We found out afterwards that the Trainer's name was Ash Ketchum, and that apparently he hails from the small hamlet of Pallet not too far from here." Annie said while gesturing out the window of Giovanni's office, which faced towards Route 1, the road that led from Viridian City to Pallet Town and vice versa.

"Ketchum…hmm, the name seems oddly familiar, though I can't seem to recall where I heard it." Giovanni also had the strangest feeling that he and this Ketchum character had met in the past, but as he tried to remember the occasion, his mind just came up blank. He couldn't seem to recall where and when he had met this boy, yet the feeling of having met him remained, a specter in the back of his mind.

"That hardly surprises us; the boy has quite the reputation as a Trainer, having reached the top sixteen in the Kanto League and the top eight in the Johto League Silver Conference as well as being an Orange League Champion. And I believe even as we speak he is about to make his run in the Hoenn League Ever Grande Conference. The boy also has a knack for playing the hero; he always seems to show up when something big is about to happen, especially when Legendary Pokémon are involved. It seems our encounter was no different. If you'd like to read about his exploits in detail, sir, my sister and I took the liberty of putting all the info we could get on him and put it in this folder for you to read at your convenience." said Annie. At this, Oakley produced a folder she had been carrying and placed it on Giovanni's desk.

Giovanni took the folder and opened it to briefly glace at it. The first thing that caught his eye was the picture at the top. It depicted a boy, no more than twelve or thirteen, Giovanni thought, with brown eyes and jet-black hair that stuck out at the sides. He had on a cap that was mostly red in color, with a streak of black running down the middle. In the middle of the black area was a design that looked like the top half of a Poké Ball, green in color. He was smiling in the photo; a smile that Giovanni thought exuded a sort of calm confidence. The rest of the report contained various bits of information regarding Ash and his known accomplishments.

Giovanni looked up from the report and stared at Annie and Oakley, a questioning look plain on his features. "And how exactly did you find this much info?" he asked, holding up the report.

"Internet." They both chorused, shrugging their shoulders as if it were the most obvious thing in the world.

Giovanni sweatdropped at this. "Err…yes, well, I'll make sure to look it over later." he said, dropping the folder on his desk before continuing "The last thing we need is idiot Trainers meddling in our affairs. But this is a matter to be dealt with another time; continue with your report."

Nodding her head, Annie continued, "Well, after Ketchum escaped with Latias, we knew that Latias would probably be on the lookout for us from now on, as well as Latios, so we figured the best course of action would be to track Ketchum as he wandered around the city. The way we saw it, Latias would eventually reveal herself to Ketchum to thank him. It's the classic damsel-in-distress routine: guy saves girl in trouble, the girl in turn falls for him. Granted, it was a long shot at best, but our instincts proved right. Latias came to Ash in human form and led him to a spot in the city that at first seemed pretty benign, although Latias proved looks can be deceiving when she and Ash, along with his Pikachu, seemed to vanish into thin air when they walked into one of the walls surrounding the courtyard. It led to some sort of garden that Latios and Latias used as a safe haven. We couldn't believe our luck; this was definitely the secret spot where the Soul Dew was hidden!"

"Waiting until night, Oakley and I proceeded to the location where the entrance to the garden was. Once inside, it didn't take long for us to be noticed. Latios and Latias engaged us in battle, but it didn't take long for their inexperience in battling to show. We were able to subdue Latios with a capture net; however, Latias managed to get away with some help from Latios. We didn't see her escape as a big deal; we could always catch her later. Right then we had more important things to attend to."

"On a pedestal in the middle of the garden, we found the Soul Dew. It was pretty obvious that this was the mystical jewel of legend, judging by its appearance alone." Anny said with a dreamy look in her eye. She remembered how the jewel had glowed with what seemed to be a blue spiritual light from within. It had been the most beautiful thing she had laid eyes upon, and when it came to beauty, Annie was an expert.

"After some prying, we retrieved the Soul Dew from its resting place. We also found some runes nearby which gave detailed instructions on how the Soul Dew activates and powers the Defense Mechanism of Alto Mare." she said.

Giovanni decided to interrupt at this moment "And what exactly was this Defense Mechanism of Alto Mare? I seem to recall you mentioning it earlier, although I don't remember it being in your mission parameters."

"Well, the Defense Mechanism of Alto Mare, or DMA for short, was a machine built many thousands of years ago. Its purpose was to protect Alto Mare should any danger arise to threaten the city. However, it was only supposed to be used as a last resort, as activating it would cause the water levels in the city to recede and would in turn destroy the Soul Dew, which, along with one of the Eon twins, was required to activate it. But don't ask me, Oakley's the real expert. Isn't that right, Oakley?" Annie finished with a sarcastic tone in her voice as she glanced at Oakley.

"Dammit, Annie, it wasn't my fault!" Oakley snapped.

"Oh, please, Oakley. Whose idea was it in the first place? It certainly wasn't me; I was content with just the Soul Dew and the Latios. It was you who decided to break mission parameters by using the DMA, and what a fat load of good it did us in the end!" Annie scoffed at her sister.

Oakley jumped out of her seat and stood facing her sister, a look of rage on her face, her hands clenched at her sides. "Do you really think I meant for it to happen like that? I keep telling you, it was the machine! It was like it was controlling me or something!" she yelled.

Annie, however, remained calm and in her seat. She smugly smiled as she closed her eyes and shook her head slightly. "I find that rather hard to believe, my dear sister. I and pretty much everyone else in Team Rocket could tell right from the start that you always wanted more, wanted to prove you were better than everyone else. You wanted the executive lifestyle, wanted to be the one to give the orders, the one in control. And when you saw the DMA, I think it gave you the opportunity you'd been waiting for; the chance for that power rush you wanted sooo bad…"

Oakley was about to angrily retort when Giovanni slammed his fist down on his desk, immediately ending the argument and causing the ladies to snap back to attention.

"ENOUGH! I will not tolerate your petty squabbles when you're in my office!" Giovanni yelled.

"Y-yes sir!" both ladies stammered nervously.

Giovanni stared intently at them to make sure his point was understood. Satisfied that they had, he leaned back and closed his eyes while rubbing a hand on his temple. "Any differences you two might have must be resolved on your own time. I can't tell you how much I do not need the extra strain right now." he said wearily.

"Very well, sir." the two lady agents chorused, although it was clear from the looks of venom they gave each other that said differences would not get resolved anytime soon.

"So…I am to gather that you went to activate this DMA, correct? And that the power of this machine caused Agent Oakley here to lose all control of her senses when she used it?" Giovanni gestured toward Oakley, who bowed her head ashamedly.

"That's the gist of it, yes sir." Annie nodded in confirmation.

"So how did you wind up in prison?" Giovanni asked.

"Well, remember when we said that Latias had escaped earlier? Apparently, she went to get help, and who better to help her than Ash Ketchum?"

"He showed up with his Pikachu and Latias, and with Latias' help, managed to free Latios and in turn, power down the DMA. When this happened, I went to get Oakley out of the DMA, but then some freak accident occurred. The DMA started malfunctioning, and in turn sealed the entrance to the DMA control center, trapping me and Oakley inside."

"The events that occurred after that are a mystery to us. It wasn't until much later that we were retrieved by the local police. In court, we were charged with reckless endangerment of the city, although I do not know how we endangered it, endangerment and attempted kidnapping of the guardians of Alto Mare, and the stealing of a precious artifact sacred to the city. The fact that we were wanted members of Team Rocket did not do us any favors. We were sentenced to 50 years in prison with no possibility of parole, and shipped off to a prison in Kanto to serve our sentence. Until we decided to escape, that is."

"And that is what happened. I hope it answers your questions." Annie finished.

Giovanni rubbed his chin thoughtfully. "I admit, it is interesting tale of events. But I must ask: What became of the Eon twins and the Soul Dew?"

"As far as we could tell, both of them survived, as we didn't observe any grieving faces in the courtroom, and the fact that we were charged with endangerment and not murder attributes to that fact. As for the Soul Dew, I assume it was restored, probably with some help from Latios or Latias." Annie answered.

At this moment, Annie decided to ask the question that she had been meaning to ask. "Sir, that fact brings us to the other reason we're here. With your permission, we'd like to have another shot at completing our mission in Alto Mare."

Giovanni was greatly surprised at this. "And why would you want to have another shot at it, seeing as you failed on the first attempt? And why should I even let you?" he asked.

Annie smiled. "Because, sir, we don't like to leave jobs unfinished. We'd also like to get payback on those two dragons for the last time. And this time, there'll be no idiot Trainers around to interfere. And I'll make sure to keep a closer eye on my sister this time, trust me." At this a vein of anger appeared on Oakley's forehead, but she managed to keep quiet. "As to why you should let us, keep in mind sir that these are two Legendary Pokémon and could prove invaluable to your future plans. As for the Soul Dew, it's a legendary artifact that the city of Alto Mare holds very dear. I'm sure that if we were to ransom it off, the city would pay any price to get it back. And I mean any price."

Giovanni hummed in thought. "You know that the police and the guardians will be watching for you, right? And that they'll probably know what to expect this time?" he asked them.

"Oh, no doubt they'll be watching for us, sir. But you forget that we're the best in the organization at what we do: remaining undetected. The police will not be a problem; they've never been able to catch us until recently. And besides, this time we won't be alone. We were hoping to have some additional support this time around to help subdue the Legendaries. I don't doubt that in the few months that have passed that they've taken care to improve their battle capabilities and might pose a problem if just me and Oakley were to take them on this time. But if we had some additional support, we'll be able to overwhelm them with sheer numbers and be able to capture them easily." Annie explained.

Giovanni pondered this for a while before announcing his decision. "Very well, you've convinced me. You will have another shot to get this right, along with the support you've requested. You will leave for Alto Mare in a few days' time. Your mission goals remain the same: retrieve the Soul Dew and subdue and capture Latios and/or Latias. And this time I'd prefer it if you stick to your mission parameters and not be sidetracked by delusions of grandeur and power." he said as he glared at Oakley.

At this, both Annie and Oakley rose from their seats. "Thank you for giving us another opportunity, sir. This time we'll make sure we don't fail you." Annie said as they both saluted and turned to leave.

"See that you don't. I don't need to remind you both that this organization does not tolerate failure lightly. I'm giving you a second chance to make up for your previous failure; do not make me regret it by failing me again, or the consequences will be…painful." Giovanni said darkly.

"Don't worry sir; you have our word that we will not fail you again." Annie said solemnly over her shoulder as she opened the door and allowed Oakley to leave first before exiting herself, closing the door shut behind her.

When they had left, Giovanni turned in his chair and idly sipped his drink as he watched the sun continue to set over the horizon, its golden glow eerily giving the sky a blood-red color as it sank beneath the trees of Route 1.


A/N: Well, I hope you liked my first chapter! Next chapter I'll introduce our protagonist, which as my summary says, is Latios.

And just to be clear, this is going to be a revenge story, so its bound to get pretty dark and brutal in the some of the coming chapters. By chapter 3 it'll probably be bumped up to an M rating, so people who do not like bloody tales of revenge should probably stay away. But if you've got no qualms against violence, then you're in for one hell of a ride! (or so I hope...)

Anyway, please let me know what you think in a review! Thanks!