So yeah, this thing. My first official Pokémon fanfiction back when I joined this site in 2007. God, this was written so long ago and it's the only one of my long fics that is even close to being finished (or at least this arc is). I haven't touched this thing since high school, geez!

Going back on it, I decided that I at least wanted to finish this. I made it part of my New Year's Resolution—I'm going to finish these projects. And since Quest started it all, I'm doing that first. 39 chapters to comb through, correct, rewrite, rework, and then (by my estimate) at least three chapters more before this is brought to a close.

Will I come back to do Johto and such? I'm not sure. My main goal is to at least finish Kanto. If I do come back, cool. If not, I can proudly say I at least brought this section of it to a close.

Will I expand it to include the other three gens of Pokémon? Not at this time. Sorry but this is staying the way it is right now. If it ever expands, that will be in the way future and I'm not looking that far right now. Sorry.

So yeah, this is my current NYR project. Expect chapters to be replaced with updated versions. I'm going to try to do this daily and keep it going so I can get to the actual chapter writing ASAP. That will take up the most time. Thankfully, I have my pal and Axl's creator by my side still to brainstorm out Axl's whole Champion battle. After that is just Kanto wrap-up and the split between areas for the main crew.

I hope you all enjoy it, if any of you are still watching this dusty old thing.

Disclaimer: I do not own Pokémon, Pokémon Coliseum, or Pokémon XD. I only own my character, Mark, and his Pokémon team.

Pokémon: Quest to Capture the Shadow Pokémon

Chapter 1: The Quest Begins

Mark Hunter grinned as he threw a Poké Ball out into the stadium. He was facing off against a trainer in a tournament in Johto. It wasn't league official, but he took any challenge thrown at him. His Pikachu, Sparks, appeared and faced off against the challenger's Totodile.

"Begin!" yelled the announcer, raising his flags.

Mark smiled and got to work. "Sparks, use Thunderbolt!"

The Pikachu charged his electricity and fired it at Totodile. It was a critical hit but the water Pokémon wasn't down yet.

"Totodile, Water Gun!" yelled the trainer.

The Totodile blasted water out of its mouth at Sparks, but the Pikachu dodged each blast. He knew what to do next. This was just another run-of-the-mill battle for him.

"Sparks, use Quick Attack and follow up with Iron Tail!" Mark ordered.

Sparks ran at the Totodile, who blasted a Water Gun to try and knock him off course. Sparks dodged and leapt into the air, his tail glowing silver. Then Sparks crashed his tail onto the Totodile's head, knocking it back a few feet. Sparks landed safely on his feet, hours of practice letting him master the technique perfectly.

"Sparks, finish it off with Volt Tackle!"

Sparks ran at the Totodile with electricity crackling around his body. The Pikachu collided with Totodile, throwing it back at its trainer and making both fall over.

"And the winner is Mark Hunter!" the announcer cried, flags waving to signal the end of the match.

"Good job, buddy," Mark said as Sparks leaped onto his shoulder.

The challenger shakily rose, returning his Totodile. "Geez, you weren't kidding. No wonder you're one of Prof. Oak's golden boys."

"Uh, I wouldn't say that," Mark said awkwardly, shaking his opponent's hand. "That might be more accurate if I did more PokeDex filling than battling…"

"Pika!" Sparks chirped, nuzzling his trainer happily.

Mark left the pre-gym in triumph, his loyal companion Sparks on his shoulder. Now he felt ready to take on the Gym Leaders here in Johto since he'd gotten a taste of the battling environment. He could already predict that this new journey was going to be a good one.

But first, he wanted check out that island he'd heard so much about—Shamouti.

It sounded pretty cool in the brochure and, if he was lucky, he might even see the legendary Kanto birds circling the nearby islands. Even luckier, he might get to see Lugia, though he rather doubted it. Lugia had only been sighted a few times in that area and those had all been during disastrous times.

But wouldn't that be just the coolest to see a Legendary Pokémon so early into his new adventure? Talk about a dream come true…

Mark Hunter walked into the sunlight beyond the pre-gym. He had dark green eyes and green hair with bangs that went in his face sometimes, the rest being bound up in a ponytail that hit his mid-back. He wore a black shirt, a red jacket with black pockets, blue jeans, and black and red tennis shoes. A red bandanna covered his head, letting his bangs poke through to drape over his forehead.

He walked over to the docks and released his Salamence, a gift he'd received during his Kanto journey months ago. Hopping on the dragon's back, Mark ordered him to fly to Shamouti Island. The dragon rose into the air and took off for the long flight to Shamouti.

Roughly an hour later, Salamence landed on the beach of Shamouti Island. Hopping off his back, Mark returned him to his Poké Ball and walked down the beach. He could already see the three islands from here: Ice, Lightning, and Fire Island, where the three legendary Kanto birds lived.

Shamouti Island was already looking like a good pit stop before his journey began. It was exotic and looked beautiful. The ocean view was fantastic. Mark wondered briefly if there was going to be a festival tonight. He could see a lot of torches further inland.

Sparks suddenly hopped off his shoulder and ran forward across the sand, cheeks sparking dangerously.

"Huh? What's wrong, boy?" Mark asked, confused.

His gaze followed Sparks until he saw a cluster of rocks further up the beach. Sparks growled, teeth bared at them. Mark tensed. Sparks didn't just growl at anything. Something was there. Something that Sparks saw as a threat…

As if summoned, a man with a Raichu came out from behind the rock cluster. He had on all black clothes and had red hair peeking out from beneath a wide brimmed hat. His eyes were hidden by dark sunglasses.

He had to be a trainer of some kind, judging by the presence of the Raichu…but something about him was bugging Mark. Something bad. What was it?

The man smirked and pointed at them. "Okay, kid, make this easy and hand over that Pikachu."

"What?" Mark replied, alarmed. "Why should I? Why do you want Sparks?"

"None of your business, kid!" snarled the man. "Raichu, use Shadow Bolt on that kid and take his Pikachu!"

The Raichu stepped forward menacingly. Its cheeks sparked and it released a powerful Thunderbolt. Mark yelped, realizing that the blow was aimed at him. Sparks instantly countered with a Thunderbolt, saving Mark from getting hurt.

"So you wanna fight back now, huh?" taunted the man. "Well, if it's a battle you want, it's a battle you'll get! Raichu, use Shadow Bolt and then Shadow Rush!"

Mark stepped back, trusting Sparks to be able to handle this. His mind was a whirl of confusion. The attacks that the man shouted made no sense. Those weren't moves that Mark recognized at all. Were those new?

And the Raichu itself…

Something about it was all wrong, but Mark couldn't identify what exactly it was. Its attacks were too powerful. He'd battled plenty of Raichu before and none of them could compare to this one. Did this guy—clearly some kind of Pokémon thief—illegally buff up his Raichu somehow? He didn't look like he was part of Team Rocket. Maybe some other organization? Mark couldn't see any identifying gang symbols on him.

The Raichu let out another explosive Thunderbolt that was countered by Sparks' own Thunderbolt. Then Raichu tackled Sparks to the ground, using its bulk to try and crush him. Sparks cried out, clawing at the larger mouse in a bid to keep from being flattened.

"Sparks, break away and use Quick Attack!" Mark called.

Sparks growled, twisting to bite at the Raichu's nearest paw. The larger mouse screeched, rearing back in pain. Sparks quickly leaped away and sped around the larger Pokémon, taking advantage of the other's weakness to try and scope out weak points on it. Then Sparks hit the Raichu with a Thunderbolt to its back. The Raichu hissed, whirling to face him in just the nick of time to block the Thunderbolt with its own attack. It struck again right afterward and hit Sparks directly, throwing the Pikachu back a few feet to roll across the sand.

"Sparks, use Iron Tail!" Mark ordered, growing frantic. He could see that his Pikachu was taking a beating out there.

Sparks got to his feet and ran at Raichu, leaping into the air as his tail started to glow silver again. But Raichu would not wait for Sparks to be ready.

It pounced, ramming into the airborne Pikachu to knock Sparks back to the sandy ground. Raichu then tackled Sparks again and hit him with a close-range. Sparks fell back and tried to get up, but Raichu rammed him again. The winded and aching Pikachu collapsed at Mark's feet.

"Sparks!" cried Mark as he dropped to his knees and grabbed Sparks, holding him close.

Laughter tore his attention away from his Pikachu.

"Told you, kid!" laughed the man, walking over to him with the Raichu following. "You should've just handed over the Pikachu and you could've saved me the trouble of beating it senseless first. Kids these days!"

"What do you want with Sparks?" Mark asked, eyeing the Raichu suspiciously. "To turn him into what that Raichu is?"

The man grinned and pulled out a gun. Mark flinched instantly. It wasn't that the sight of a gun was so shocking. Guns were just as prevalent in the world as Pokémon were. It was the sight of a trainer making use of one that was surprising. Most gangsters and evil organizations never bothered with guns because they used Pokémon for their dirty work.

This guy—and whoever else may be with him—clearly preferred to use both to get their job done.

"Precisely," the man said. "We'll turn that Pikachu into a Shadow Pokémon."

"Shadow…Pokémon?" Mark repeated.

The term didn't sound familiar. Was that a new kind of Pokémon? Clearly it was an artificially engineered one, if Mark had to guess. No regularly raised Raichu could be that immensely strong.

It made him worry about what could happen to Sparks if such a thing was done to him.

"That's right. Pokémon who have had their hearts closed," the man said smugly, passing the gun between his hands idly. "They have an advantage against all Pokémon and their attacks are effective against all types. They're even resistant to their own type, which is the reason your Pikachu couldn't beat my Raichu. They're the ultimate tools for world domination on a scale that no other group could ever hope to reach."

Mark felt the cool metal of the gun against his forehead. The man wouldn't stop smiling down at him.

"There's one Shadow Pokémon of each species in the PokeDex, except for the legendaries…for now. Master's working on that," the man said, smirking. "Soon we'll have the whole world bowing to us. To Cipher!"

"Then why do you need Sparks? Don't you already have a Shadow Pikachu?" Mark asked, looking at the weakened Pikachu in his arms.

He filed the information he was hearing away. If he survived this, he'd need to get this to the police pronto. Whatever this Cipher group was, they were seriously bad news.

"Yeah, we do. But I could always use another Pikachu as fodder." The gun was pressed firmly against Mark's forehead now. "And now that you know all of this, I'll have to kill you. Say good bye, brat!"

The man's fingers started pulling the trigger. Mark tensed. So much for running to the police…

A loud shriek tore through the air and a blast of fire crashed into the ground near them. The man jumped back, head snapping toward the sky, while Mark stayed there in shock. Circling above them, letting off Sacred Fires and Aeroblasts, were two of the most iconic Pokémon in all of Johto—Ho-Oh and Lugia.

All of these attacks were clearly aimed at the man, not Mark. He had his Raichu defend him with bursts of lightning, but it was tiring quickly. Sparks had managed to do enough damage to it during their fight. And up against two Legendaries, even a beefed-up Raichu couldn't win.

"Pi…ka…" Sparks squeaked.

"Sparks, you'll be okay," Mark said, fumbling for his Poké Ball. "I'll get you to the village. There's gotta be one here. Somebody can help you."

"Pi…" Sparks shook his head and tried to crawl off of his trainer's lap, a paw extending past Mark's knees. "Pika!"

"Huh? What are you…? What the heck?"

Mark looked where Sparks pointed and noticed a necklace was lying in the sand in front of him. It clearly hadn't been there before, if Mark's memory was right. It was a small black ball the size of his thumbnail with a silver feather bordering one side of it and a rainbow feather on the other. It was on a gold and silver chain. It was certainly beautiful.

Mark shuddered. He had a weird feeling about this necklace. Some inner voice spoke to him, telling him that this was his. Though nervous, Mark grabbed it and carefully put it around his neck.

As soon as he did, he looked at the scene before him and saw that something was different.

The Raichu! It didn't look normal at all.

Its coloring was all wrong. Instead of having brown paws, they were black. Instead of having a yellow cheeks and lightning-bolt tail, they were red. And its eyes were glowing red, like nothing Mark had ever seen before.

The real kicker was its aura. The Raichu looked like it had a cloud of shadow wreathing it. It was a wispy purple-black cloud that swirled and clung to the large mouse's form, accenting its darker colors. Mark could suddenly understand why it was called a Shadow Pokémon now.

When he carefully took the necklace off, the Raichu looked normal again.

Putting it back on, he felt warmth coming from the necklace. He looked down and saw it was glowing vibrantly. With a squeak, Sparks suddenly rose without difficulty. The Pikachu's injuries were healing!

Mark then realized what was going on.

The feathers on the necklace! They were Ho-oh and Lugia's feathers. That's what had to be healing Sparks.

Which meant that the black bead at the center…was what was letting him see these strange Shadow Pokémon in their real forms.

Standing back up, Sparks jumped out of his arms. Lugia and Ho-oh disappeared abruptly into the clouds, leaving the man and his Raichu alone. Sharp clicking signaled that the gun had been emptied of its bullets during the panic.

"You! You did that, didn't you? Calling Legendaries on me! You pesky brat!" the man accused wildly. "Raichu! End this kid!"

His Raichu immediately launched a Thunderbolt—no, a Shadow Bolt, Mark could now see the darkness that coated the lightning and made it so explosive—at Sparks, who easily dodged it. Mark wasn't sure if Sparks could see it to or if the Pikachu was falling more on instinct to evade being hit. Whatever it was, it was working.

"Sparks, use Iron Tail and follow up with Thunderbolt!" Mark yelled.

Sparks leaped into the air and smashed his glowing tail down on Raichu's head. Hopping a safe distance away, the Pikachu used Thunderbolt on Raichu. An explosion ensued and, when the smoke cleared, the heavily weakened Raichu was down, struggling to rise.

The man went crazy, shouting and yanking his hair. He turned, racing away across the sand in a mix of rage and terror. "How could a kid beat me and my Shadow Pokémon?! You remember this, kid! Cipher will be after you for this! Remember!"

Mark watched him run, not sure if he should pursue or not. He decided against it. Though empty, the man still had a gun. It was probably best to clear out now before that guy came back.

That left the man's Raichu, lying in the sand, alone and injured.

"Weird. Did he abandon his Pokemon?" Mark asked, looking down at the Raichu in pity. "For a guy who claimed his organization only had one of you, he sure was fast to ditch you."

He couldn't just leave it lying there. What if it died? And it was foolproof evidence of what this Cipher organization was doing. He had to take it to the police.

But how?

Another feeling washed over him. It had to be coming from the necklace. It told him to catch it. But…that was impossible. You couldn't catch other trainers' Pokémon! It was against the law!

Then again, he had no proof that that man had caught this Raichu at all. It was worth at least checking, right?

Mark sighed and grabbed a Poké Ball, tapping it against the Raichu's limp frame. The Poké Ball opened and the Raichu disappeared in a flash of red light.

"I guess he didn't catch it?" Mark muttered.

He still felt bad about this. The Raichu wasn't his. He shouldn't be catching it. What if the police decided he was a thief?

Mark picked up the Poké Ball and jumped when it suddenly began to change. The red part darkened to black and the white part became gray. A jagged red 'S' appeared on the black part, right above the button. It was like an entirely different kind of Poké Ball now.

He'd never seen a Poke Ball like this before. Was this also related to the necklace?

Was the Raichu inside still okay?

"Uh… Come out, Raichu," Mark said, opening the Poké Ball.

The Raichu popped out, still injured but conscious. It swayed slowly on its long feet, looking dazed. Mark sighed in sadness and picked it up in his arms.

The Raichu suddenly smirked and shocked him with a blast of shadowy electricity.

Mark cried in shocked, instantly tensing for the pain…and then realized that he felt nothing. The attack…wasn't working?

His chest felt warm. The necklace was glowing white and the attack faded from existence. The Raichu was confused and fell limp in Mark's arms, burying its face into his black shirt. It looked angry and ashamed.

Mark breathed a sigh of relief. Sparks used to electrocute him a lot back when he was a beginner. He knew what electricity felt like. He was glad that he was able to avoid this buffed-up version of a standard Thunderbolt.

A loud shriek was heard overhead.

Mark jolted, looking up to see Ho-oh heading right for him. He yelped, racing further inland to avoid becoming a landing pad. Ho-Oh landed lightly in front of him, rainbow wings folding elegantly against its large frame. Lugia landed beside the Ho-Oh and glanced at the Raichu, a troubled look on its draconic face.

Then the Ho-Oh spoke.

"Get on."

Mark was confused. "What? Why?!"

He'd heard of the telepathic abilities of Legendary Pokémon. It was popular in myths and stories, but never having run into a Legendary before, Mark had been iffy about that. Now he knew for sure. It was actually quiet terrifying.

Sparks darted away from him, running up Ho-Oh's wing and resting on its shoulders just behind its neck. "Pika pi!" he cried, waving a paw as if to invite his trainer to join him.

"You will not be harmed, but we need to speak with you," Lugia stated. "Get on."

Mark sighed in defeat. This was a losing argument, that much he recognized. He walked over to the Ho-Oh, climbing onto its back when the birds lowered itself. He sat behind Sparks, gripping the rainbow feathers with one hand while his free arm wrapped around the Raichu huddled against his chest.

"Hang on," Ho-Oh said.

Then Ho-Oh took off with a monstrous flap of its wings. Mark clung to the feathers on its neck while Raichu clung to his shirt. Sparks hung onto the feathers too. Soon the two Legendaries were flying high over the ocean, flying away from Shamouti and its surrounding islands.

"So, you wanted to talk. If you know anything, I at least want to know why that man attacked me," Mark said, hoping that they had the answers.

"Just as he stated: to have another Pokémon to mess with," Ho-Oh replied.

"Well…" Mark started, glancing at the Raichu clinging to his shirt. "Who is Cipher? And what are they doing to make Pokémon into…Shadow Pokémon? What are Shadow Pokémon, anyway?"

"Cipher is an evil organization dedicated to closing Pokémon's hearts and turning them into battle machines," Lugia responded, tone cold and bitter. "They've done this twice before in the past, in a far away region called Orre, and failed. Now they're doing it again, moving from the isolated Orre into more populated regions to expand their reach."

Mark frowned. He'd never heard of a place called Orre before. He made a note to look for it on the next world map he saw.

"Shadow Pokémon are unusual. With their hearts closed, they've become violent creatures whose sole purpose in life is to fight and win by any means necessary," Ho-Oh said, sadness in its voice. "All of its original moves are forgotten and replaced with Shadow moves, bypassing all type advantages to equally hurt any Pokémon that opposes it. They can't level up, evolve, or learn any new moves beyond the ones Cipher has implanted in them. These moves can even cause the Shadow Pokémon to possibly hurt themselves in battle."

"Cipher has implemented their plan by expanding their own numbers. They have corrupted over four hundred Pokémon with their cruel science," Lugia said. "I have witnessed their acts with my own eyes. They must be stopped at once before they consume the entirety of the planet. But we Legendaries can only do so much. We ourselves are at risk for capture by Cipher now. That is where you, human, come in."

"Wait! Me? Why me?" Mark asked. "Why are you telling me all of this? I may have caught this Raichu, but I can't catch over four hundred Pokémon! That's insane! You need to tell the police or something! Really strong trainers!"

"We don't have that much time, human! You'll have to do for the moment. If you wish to inform your governments, then do so," Lugia said. "But right now, you are all we have. Your mission is to save the Shadow Pokémon from Cipher's evil clutches and purify them. You must steal back the ones who are being abused by criminals and open their hearts again. Anyone else who sees them won't know they are Shadow Pokémon. Only you can see them, human."

"But how?" Mark asked, confused and overwhelmed by the task set before him. "How do I stop Cipher? How do I purify the Shadow Pokémon? You aren't telling me everything!"

"That," Ho-Oh said as they flew lower. "You will have to discover on your own, human. Use the Snag Balls to capture them and then find a way to purify them. If you open their hearts, they will be free from Cipher's influence!"

Mark groaned, suddenly feeling queasy. This whole mission sounded like a big pot of trouble. Did he really want to get involved in this? He just wanted to journey around Johto with his team and have some more fun.

Mark looked down past Ho-Oh's wing and saw none other than Kanto below them. That made him jolt. What were they doing here? He'd gone to Johto to get away from Kanto for a while!

"Why did you bring me here?" he demanded, unfairness welling in his chest.

"We sense many Shadow Pokémon residing here," said Lugia. "You must find them and catch them. We can do no more for you now, human."

"Wait, you're just leaving m—AAAAAAAAHHHHHHHH!"

Ho-Oh abruptly swung its body sideways, throwing Mark off and sending him falling into open air. Sparks cried out, flapping his paws frantically. Mark stared up at the circling Legendaries in shock and betrayal.

"Good luck, human!" the two Legendaries cried.

.o.o.o.o.

Mark landed in a huge pile of hay. It wasn't the most comfortable landing ever, but it beat hitting the ground. Looking up gave him no sign of either Johto Legendary. He was alone in a hay field with his Pikachu and a battered Raichu.

"Oof! Nice landing, eh?" Mark grumbled. "What were they thinking, letting me fall a couple hundred feet in the air? They're lucky I landed here! Right, Sparks?"

His Pikachu nodded, flopping onto his chest. The Raichu was by his side, breathing heavily from the sudden drop. Mark sighed and returned it to its Poké Ball—a Snag Ball, as Ho-Oh had called it. Putting it on his belt, he slid down the hay pile with Sparks.

After picking the hay out of his hair and clothes, Mark looked towards where the sun was setting. Sparks pounced on his jacket and grabbed at a thin rectangular object sticking from his pocket. It tumbled to the ground.

"What's that, Sparks?" Mark asked. He didn't recalling having anything in his pockets.

"Pika pi!" Sparks said with a look that said 'How should I know?'

"Hey," said Mark, picking it up. "I know what this is! This is a PDA, a Pokemon Digital Assistant! This thing stores massive amounts of data and holds a ton of personal information on it. But these are expensive as heck! How did I get one?"

He turned it on. It worked just fine. It wasn't registered to a user, so it was clearly new. He checked the menu screen and saw something that he'd never seen before.

"A Shadow Monitor? What's that?"

Mark turned the application on. A bunch of lists and windows popped up. After doing some sifting around, Mark felt elated. The Shadow Monitor had a list of all the Shadow Pokémon, showed who they were being carried by, and where they were at the moment.

"Awesome!" Mark cried in joy.

"Pikachu?" squeaked Sparks, looking confused at his trainer's happy face.

"Sorry, Sparks, it's just that…" Mark grinned, petting Sparks' head. "It's just that with this thing, everything is a lot easier. I know where they are, their level, attacks, trainer, everything! I can actually preplan some of this stuff! Maybe this won't be so hard after all…"

"Pika pi! Pikachu!" Sparks cried, leaping on his shoulder.

"Alright then, Sparks! Let's go catch some Shadow Pokémon!" Mark said, walking along a path through the field of hay piles. "But first…"

He picked up Raichu's Snag Ball and looked it over. He knew it was essentially forbidden to capture another trainer's Pokemon, but the criminals using the Shadow Pokémon were leaving him no choice. And it was for the good of the Pokémon, right?

Surely the police, and anyone else who saw him doing this, wouldn't be mad. He was doing a good thing, right? This was saving innocent Pokémon. It had to be okay.

Half an hour of walking led him to finding a city. It wasn't very big. It was even familiar. Mark entered the Pokémon Center, which informed him that he was in—where else?—Viridian City.

It was like starting his Pokemon journey all over again but, instead of catching normal Pokémon, he was catching Shadow Pokémon and trying to stop some evil organization intent on complete world domination.

Mark rented a room for the night in order to rest. Hopping into bed, Sparks fell asleep instantly. Mark, on the other hand, stayed awake for a few more hours, trying to figure out how this was all going to work.

Should he really go to the police? Should he backtrack to Pallet Town and find Prof. Oak? Tell a Gym Leader? Or should he forge ahead and try doing this alone?

When 2AM rolled around, Mark ended up falling asleep with thoughts of how to purify Raichu. His dreams seemed to say that his PDA would tell him how to purify them, but how truthful were dreams? Maybe it did, but he'd have to figure it out in the morning. Right now, Mark needed sleep more than anything else.

That night, his dreams were filled with claws, fangs, blood, shadows, and screams. It was not a pleasant sleep.