I came up with this story after coming across a hack with a similar idea for FireRed and LeafGreen. I've got plenty of scenes thought out for this story but this will only be updated when I have free time after updating my PMD2 and Shadow Pokemon stories. I hope you enjoy it anyways.
Summary from my profile: Tory, a new recruit for Team Galactic, is poised to fight against the forces of good. After encountering Prof. Rowan, stealing a Turtwig from his briefcase, and battling new trainer Cass and Pokemon assistant Marie, he flees back to Veilstone with his prize. After obtaining a stolen PokeDex and five Poke Balls from Cyrus, Tory is given a mission to continue following Cass and keep tabs on his activities. Agreeing, Tory heads for Twinleaf Town and begins his mission to follow Cass. Along with fighting Cass and other grunts to go higher in the Galactic ranks, Tory starts to understand Cass' goals and relates them to his own. As time goes on and Cass beats more and more Galactic members, will Tory's allegiance slowly change as his need to help Cass increases? And what will Cyrus think of the possible betrayal by one of his best agents?
Pokemon: Sinister Darkness
Two Galactic grunts are walking down the hallways of the Galactic Veilstone Building, muttering to each other. Their voices echo off the metallic walls along with the thudding of their boots.
"Why do we have to deal with the new recruit?"
"Because the boss said so."
"But it's not fair to us!" the first complained. "I have better things to do, like steal some brat's Pokemon!"
"I know, I know. But the faster we get this done, the faster we can get back to our normal routine." The second reassured. "We're here." Pulling out a key with a G on the handle end, he inserted it into the doors and turned it. The doors swung open and the duo stepped into the room. They fell to one knee and bowed their heads. "Sir, we've come to carry out your orders."
A man with spiky blue hair smiled and nodded. He pushed a young boy around 10 years old toward them. He had the same blue-green hair cut in the Galactic grunt fashion as all the grunts had. Blue eyes shined with curiosity and mischief. He was wearing the standard Galactic uniform. "Boys, this is Tory. He's yours to keep an eye on for his first mission." The man said. "Keep an eye on him and don't let him get caught. Jump in if you need to."
"Yes, sir," the first grunt replied. "What's his mission?"
"To head for Prof. Rowan's lab and steal a Pokemon. Which Pokemon, I don't care." The man explained. "Find Rowan and steal the Pokemon, by force if necessary. If Tory succeeds in this mission, it will mean rewards for the three of you. Understood?"
"Yes sir!" All three saluted, heading out the doors.
Exiting the Veilstone Building, the second grunt pulled out a Poke Ball and released a Staraptor. "Staraptor, use Fly and take us to Sandgem Town." He ordered.
Staraptor screeched, spreading its wings. The trio was surrounded in a white light and Staraptor shot into the sky. The three Galactic Grunts were flying through the sky beside Staraptor, soaring past cities, towns, and routes at high speed. After a few minutes, they stopped at a peaceful little town in a forest. Returning Staraptor, the trio headed for a large building in the northwest corner of the town.
Kicking the door in, they entered. A quick scan of the place told them it was empty. "I'll look for the briefcase!" the first grunt said, wandering deeper into the lab. He returned a minute later, stuffing something into his pocket. The second grunt didn't notice but Tory did. "Nothing. He must be somewhere else."
"Hmmm..." Tory hummed. What did he put in his pocket?
"Hey, look at this." The second grunt called, pointing to a calendar tacked to the wall. "It says 'Visit Lake Verity' and it's on today's date!"
"Then we're off to Lake Verity." The first grunt nodded. "Come on, Tory. The faster we finish this, the faster we can get out of here."
Leaving Sandgem behind, they headed for Lake Verity on foot. The two older grunts fought the wild Pokemon while Tory observed. I'll be fighting like that one day. Once I steal this Pokemon, I'll get one of my own and get stronger. I'll be the best Team Galactic has ever seen! Reaching Lake Verity, Tory spotted the briefcase. "There it is!"
Prof. Rowan, his assistant, and a young trainer were standing near it, arguing over something. Tory quickly ran toward the briefcase and grabbed the only Poke Ball inside. "Got it!" he cried.
"Hey, what are you doing?"
Tory slowly turned around to see the trainer standing behind him. He had short red hair with long bangs and brown eyes. He wore a brown and red short-sleeved jacket, black tank top, faded blue jeans, red and white tennis shoes, and a black bandanna around his head. He had a Poke Ball in his hand.
He must be a Pokemon trainer, Tory thought. But he only has one Pokemon. He must be a new one. This'll be too easy. "Nothing," he replied coldly. "Why?"
"Nothing?" an old man, Prof. Rowan, barked. "Why, it looks like you're stealing one of my Pokemon!"
"So what if I am?" Tory said, standing up and backing away. "What are you gonna do about it?"
"We'll battle you, that's what!" a girl with short black hair and blue eyes cried. She must be Rowan's assistant, Tory confirmed. "Chimchar, come on out!"
"You too, Piplup!" the new trainer yelled.
A brown monkey with fire as a tail and a blue penguin Pokemon jumped out, ready to fight. Throwing his Poke Ball, Tory prayed for a powerful one. A green and brown turtle Pokemon came out, jumping around happily. "Okay, attack!" Tory cried.
"Chimchar, use Scratch!" the assistant ordered.
"Piplup, use Pound!" the new trainer added.
The turtle cried out as the attacks hit it. "Ugh!" Tory groaned. What do I do? If only I knew what Pokemon this was, I could win this. Oh well...When in doubt, use Tackle! "Use Tackle!" the young grunt cried. Almost instantly, the turtle crashed into Piplup and knocked it down. "All right!"
"Piplup, use Pound again!" the trainer said.
The penguin got up and attacked, throwing the turtle down. The monkey leapt forward to finish the fight with a Scratch. Tory raced forward and grabbed the turtle, yelping when Chimchar's Scratch tore along his side. Collapsing, the duo was beaten. I can't believe I lost, he thought sadly. My first battle and I lose so badly. What a great way to impress my superiors...not!
"Hey, are you okay?" Opening his eyes, he saw the new trainer standing above him. "Why were you trying to steal Prof. Rowan's Turtwig?"
"I was ordered to, that's why." Tory grumbled, sitting up. His side ached but there was no blood. Returning the turtle, Turtwig, to its Poke Ball, he stood up shakily.
"Alright, boy. That's quite enough." Rowan grunted. "Now give back Turtwig and you can leave without me calling the police."
"No chance, old man!" Tory yelled, bolting. He ran down the path to Route 201, clutching Turtwig's Poke Ball close to his chest. Reaching the two older grunts, Staraptor used Fly to get them back to Veilstone. Tory never looked back, only looking at his new prize, Turtwig. I may have lost the battle but I won the war. Turtwig is MINE!
After landing back in Veilstone, the trio went to the top floor the report their mission to the head of Team Galactic. Entering, the trio presented the Turtwig to the boss. "Tory was successful in retrieving a Pokemon from Prof. Rowan. He engaged in battle with Rowan's assistant and a new trainer, losing miserably. But he managed to escape with the stolen Pokemon." One of the grunts reported.
"Aside from Tory's defeat in that battle, the mission went smoothly." The second goon added. "What are our rewards?"
The first elbowed him in the gut. "Stupid bonehead!" he hissed. "If we've done a bad job, please give us a punishment as you see fit."
"Well..." The boss turned away, glancing at the Poke Ball holding Turtwig. "Tory, you shall stay behind for your reward and your next mission. You two, your rewards reside in your offices. You may leave."
Rising, the two older goons fled. The boss stepped forward and handed Tory back Turtwig's Poke Ball. "Huh? Why are you giving me it back?" Tory asked.
"I have a very special mission for you, Tory." The boss replied. "I have a feeling that the trainer you told me you lost against may have something to do with us in the future. As well as letting you get stronger, I want you to keep tabs on him. Record all of his battles, all of the Pokemon he's captured, where he goes, who he knows well."
"You mean, follow him around?" Tory asked. "But I'm guessing I'm not supposed to get caught, right?"
"Correct," the man nodded. He handed Tory five Poke Balls and a PokeDex. "This PokeDex is one that I had stolen a while ago from a careless trainer. These Poke Balls are so you can capture more Pokemon. This mission depends entirely on you. Don't fail me, Tory. The consequences are great if you do."
Tory gulped, accepting the Poke Balls and PokeDex. "Yes sir. But...where should I go now? Should I go looking for him?" he asked.
"Your subject is probably still in Twinleaf Town, preparing to head for Sandgem. He might have more Pokemon on him now than he did in your first battle. To make things a bit more interesting, battle him once in a while. I'm sure you two boys are looking for rivals, so I'm sure you'll find one in each other."
Tory nodded. I'm not letting him get away with beating me. I'll show him who's boss in the next battle we have. I promise! "Yes sir! But how do I get there?"
"You'll be escorted there by your two friends, the grunts that went with you on your first mission. Once there, start following him and track his movements. It is possible that you may have to fight fellow grunts in order to achieve this."
"Yes sir. I'll leave right away." Tory said, backing away.
"Good luck. Remember, Tory..."
"...Yes, sir?" Tory asked.
"The first rule in following a subject that may need to be terminated: NEVER get attached to the subject. Understood?"
"Sir, yes sir!" Tory saluted. Like hell I'll ever get attached to a kid like him. I'd sooner leave Team Galactic before I get attached to anyone! He turned and ran to the bottom floor, meeting the two grunts. It only took a second to realize that they were higher rank now. "Are we ready to go?"
"Of course!" the first grunt laughed.
"Don't fail, got that?" the second spat.
Tory shivered, intimidated. "Yes sir!"
"Then let's go!" the second grunt cried, releasing Staraptor. Using Fly, they reached Twinleaf in no time. "See you later, brat! Have fun!"
Have fun? How do I do that? Tory wondered, looking around. Spotting a nearby house, he went in and discovered that it was empty. My uniform stands out way too much here. That redhead will find me in seconds if I keep wearing it. Keeping a close eye out, he quickly changed into his old street clothes that he had worn earlier before being recruited into Team Galactic.
Stepping out of the house and walking to the pond at the south end of the town, he peered into the water to check his hair and clothes. He was wearing a dark blue sweatshirt with white edges and a pale blue front pocket that he could put both hands into, black jeans, blue and white shoes, and a blue and white-striped cloth wristband around his left wrist.
"Now to find that trainer," he muttered, walking around. There were only four houses, making it easy to pinpoint his target. The redhead was speaking to a blonde boy and a raven-haired girl. "Bingo!"
He crept closer and listened in on the conversation. "Why did my Pokemon have to be stolen?" the blonde complained.
"Calm down, Ken." The raven-haired girl reassured. "Prof. Rowan is searching for that kid as we speak. By the way, until he finds that kid, you could still have Cass fight a Pokemon until it's weak enough for you to catch. That's not against the rules."
"But Marie!" the blonde, Ken, whined. "I want to catch my first Pokemon by myself! I don't need Cass' help!"
"Fine, suit yourself." The redhead boy, Cass, shrugged. "Wait around until Rowan finds your Turtwig...if he ever finds it. I'll get going to Sandgem and catch some Pokemon. See you!"
As Cass headed down the path, the blonde dashed toward him and grabbed his arm. "Fine, you can help me catch something!" he groaned. "Just make sure it's not a weak Pokemon!"
Cass smirked. "Okay, Ken. If you say so."
As the two boys headed for Route 201, Tory quickly followed after them to begin his mission. As he passed Marie, she noticed something and said, "Hey! You're not from around here, are you?"
"Huh?" Tory asked, surprised by the question.
"You're not from around here, right?" Marie repeated. "I've never seen you before. Who are you?"
"Tory," he replied, making sure his hood was hiding his hair. "My name's Tory and I'm just passing through. See you." As he stalked away, he was certain that the assistant was confused by his behavior. Stupid girl, he thought. You better stay out of my business unless you want to get hurt.
He walked along Route 201 until he saw the two boys again. Cass had just weaken a Starly and Ken was preparing to catch it. Tossing the Poke Ball, the Starly was captured. Ken danced around, cheering. "I caught my first Pokemon!"
"With my help, of course." Cass added. "Now, if you'll excuse me, I have to head for Sandgem Town. I have more Pokemon to catch and an angry Prof. Rowan to talk to."
"Hang on, I'm going too!" the blonde protested. "But I'm gonna level up Star first."
"Star? You're naming it Star?" Cass asked.
"Yes, because she's the star of my team!" Ken cried, pointing to the sky. "She'll be my strongest Pokemon ever!"
"Um, okay..." Cass muttered. "I guess I'll level up my Piplup too."
"You're not giving it a nickname?" Ken asked.
"Uh, no. I guess I'm not." Cass replied.
A nickname? Tory thought.
"Don't you know that giving your Pokemon a nickname will help them bond with you better?" Ken demanded. "I'm gonna nickname all of my Pokemon and make them love me so they'll get stronger just for me!"
"I swear you're nuts, Ken." Cass chuckled.
"Am I not nuts!" Ken yelled. "I'm just passionate about Pokemon training, that's all."
Should I give my Turtwig a nickname? Tory wondered, pulling out Turtwig's Poke Ball. But what would I call him? Turty? Shelly? Um...Twiggy? Yeah, that sounds right! His hand rested on Twiggy's Poke Ball. "Hey, Twiggy. Ready to start our mission?" he whispered.
While Cass and Ken leveled up in the grass patches close to Sandgem Town, Tory leveled up a little closer to Lake Verity and Twinleaf Town. By the time he noticed Cass and Ken heading for Sandgem Town, Twiggy had grown to be Level 10 and learned Absorb. The Galactic grunt-in-training quickly followed after the trainers.
Once they reached Sandgem Town, Ken ran into the lab while Cass entered the Pokemon Center to heal his Pokemon. Tory quickly followed Cass and healed his own three Pokemon. While leveling Twiggy up, he'd captured a Starly and a Bidoof. Feather and Bido were his nicknames for them. After having them healed, he quickly followed Cass back to the lab.
As Cass was entering the lab, Ken came rushing out. "Hey, Cass! Gotta go, see you later!" With that, the blonde raced away.
Marie came out and shook her head. "He's really impatient, isn't he?" she asked Cass. "He even forgot to grab his PokeDex."
"PokeDex?" Cass repeated, confused.
"Oh, come inside!" Marie said. "Prof. Rowan has a surprise for you!"
Tory patiently waited outside while Cass entered the lab. "This isn't so bad, actually. It's like being on a normal Pokemon journey, except I have to follow some brat around and prevent them from stopping Galactic's future plans."
It was getting dark when Cass came back out. The redhead headed for the Pokemon Center to rent a room for the night. Waiting until Cass was out of sight, Tory entered and rented a room too. Getting ready for bed once he entered his room, he stopped in front of the mirror. I definitely have to do something about my hair, he decided.
Crawling into bed, Tory fell fast asleep. Cass, on the other hand, was having trouble sleeping. It's funny but I feel like I'm being followed, he thought, opening his eyes and staring at the ceiling. I wonder if I'll ever see that strange boy again. The one who stole Turtwig...Is Ken and Marie okay, too? Sighing, he closed his eyes again. Exhausted from the day's events, he fell asleep.
--
So, what do you think so far? Not much, I know, but more will come when I have time to update this. What will Tory do with his hair? And will Cass figure out who's following him? I hope you enjoyed it. Please review!