A Note from Rappkea

Hello, Internet, and welcome to my newest fanfiction. Some things before you begin reading. First off, this story is a sequel to Pokémon: XD Gale of Darkness and will contain a lot of references to Pokémon Colosseum as well. While I am a firm believer in not spoiling things for people and while I wish that my readers would play the two games before reading this fanfiction, I have wrote the entire two games in a nutshell for the prologue. Secondly, I know this is the third story that I have in progress. I just have a lot of ideas going on and I want to get them out and get them started. Also so I don't get bored of writing only one story. While I have three stories going on, if you wish for me to focus more on a certain story then please just PM me and let me know which one you want me to write more of. And lastly, for this story, I need a team of six Pokémon for the protagonist. I would like for readers to suggest Pokémon that could go in this story. Simply tell me in the comments below and I will try to put it in somewhere. Thank you, and enjoy.

Disclaimer-I do not own Pokémon or any of the characters or Pokemon in the game. That is the property of Nintendo etc.

Prologue

Today, I am going to tell you a legend, one that has been spoken of for the last 10 years. This is the legend of Orre.

Our story starts ten years ago, in the desert region of Orre. Deep in his laboratory hidden in the middle of the desert, a wicked man by the name of Ein, discovered the method of shutting off a Pokémon's heart. It would turn the Pokémon from an innocent creature into an evil fighting machine. When he completed his process he tested it on his most powerful Pokémon, Raikou. When the process was complete, Ein tested his Pokémon. His machines in his lab found an invisible, black and purple aura coming from Raikou. Ein was pleased with his experiment as his Raikou was turned into a Shadow Pokémon.

Ein presented this data to his master, Evice. Evice was the mastermind behind the criminal syndicate known as Cipher. Cipher saw Pokémon as only tools, used only to complete the goals of their master and with this new Shadow Pokémon, it would become easy for Cipher to obtain world domination. Once, the Shadow Pokémon process was completed, Evice had Ein turn his Tyranitar into a Shadow Pokémon and it powered up his Pokémon. Evice was pleased as well and he then had Ein mass produce Shadow Pokémon.

With the production of Shadow Pokémon in full swing, Evice assigned his second in command, Nascour to see to it that no one could stop him and his Shadow Pokémon from taking over the world. Nascour, with his Shadow Metagross, enlisted the help of four Cipher Admins: Miror B., Dakim, Lady Venus, and Ein. They were to ensure that the Shadow Pokémon plan would be carried out.

One thing that Cipher didn't account for was that the process could be reversed. By using the pure power of a Pokémon named Celebi, a Shadow Pokémon's heart could be reopened with the power of a mystical rock called the Relic Stone. The great Pokémon god, Arceus, foresaw the dawn of the Shadow Pokémon and told Celebi to create a pure sanctuary Where a Shadow Pokémon could be purified. This is the reason why Celebi created the Agate Forest and the Relic Stone. Agate forest was in the northwest region of Orre where everything was lush and fruitful and where life prospered. Soon, villagers found the Agate Forest and began to settle there and it was renamed the Agate Village.

One bright day in Agate Village, one young man by the name of Eagun was exploring around Agate Village with his loyal companion, Pikachu. As they walked around the village, Pikachu suddenly took off running. He ran down a small ramp and disappeared into a cave. Eagun followed his friend into the cave and he emerged in the Relic Forest. It was so calm and peaceful and it was surrounded by many tall trees and despite being underground, a blue sky could be seen. And in the center of this mystical place, was a stone pillar that Pikachu was sitting next to.

As Eagun approached the stone pillar a green light emanated from the rock and a small green fairy emerged from the Relic Stone. She flew up and flew in circles around Eagun. She stopped in front of the young man and then flew over to the stone pillar in the middle.

Eagun approached the tower and put his hand on the rock. Suddenly, light green writing appeared on the rock. It read, "Eagun, descendant of Reginald and Penelope, You have been chosen by the great god, Arceus to take on a great task."

Eagun was astonished. A great task? He looked at the legendary Pokémon. "Why me?" he asked. The writing under his hand suddenly faded and more took its place.

"You have been known to be pure of heart and that purity is needed. An evil organization is going to alter Pokémon and their hearts and turn them into fighting machines," the writing on the stone said.

Eagun looked at Celebi and then at Pikachu. "I am not trainer. How can I save Pokémon if I can't battle this organization?"

Celebi smiled and the writing changed again. "Do not worry about that. A chosen trainer will come to Agate and he will save these Pokémon."

Eagun nodded and Celebi nodded back. Eagun felt the writing change. "Now, return to your home and do not forget what you have seen here."

Eagun nodded and did as the legendary Pokémon asked.

As these events transpired, Cipher was moving right along with their Shadow Pokémon plan. The problem being is that they needed more Pokémon to turn into Shadow Pokémon. To fix this, Nascour turned to the help of Team Snagem. Team Snagem was a no-good gang of thieves led by their boss, Gonzap who agreed to Nacour's terms. Nascour wanted Team Snagem to steal or snag Pokémon from other trainers to convert them into Shadow Pokémon. Over time, Cipher feared that Shadow Pokémon could one day be used against them so Nascour gave Team Snagem two technologically advanced devices called Snag Machines. One was a giant device that looked a lot like a vending machine but it could turn ordinary Pokéballs into special ones called Snag Balls. They could actually snag a Shadow Pokémon from another trainer, even if it was already owned by the trainer, although it only worked on shadow Pokémon. The other Snag Machine was more like a piece of armor that fit over the user's left arm. Other than being form personal use, it served the same purpose as the other Snag Machine.

While this new partnership pleased most people in Team Snagem and Cipher, it did not please one member of Team Snagem by the name of Wes. Wes was a tall dark and handsome type. He had grey hair even though he was only 22 years old. When he wasn't wearing his Team Snagem uniform, he always wore a black under armor shirt and pants with a blue coat over it. He was most famous in Team Snagem for his Espeon and Umbreon and he was the team's best trainer. When he heard that Team Snagem would be joining with Cipher, he was appalled.

He didn't want to be a part of this and more importantly, he didn't want Team Snagem to be in league with Cipher. So one morning, he snuck out of the base bright and early with his Espeon and Umbreon and got on his motorcycle. He hid his ride around the corner of the canyon that Team Snagem's base was hidden in. he used the remote in his hand to activate a bomb that he hid in the base. An explosion could be heard throughout the entire base. Wes was pleased with his handiwork. Leaving Espeon to guard the bike, Wes and Umbreon ran towards the hole that he made in the wall of the base. Fortunately, the room that had the destroyed wall was the room that had the small personal Snag Machine. He took it off of its stand and then he and his Pokémon companion ran for their lives. Luckily, they reached the motorcycle before any Team Snagem members caught them. Gonzap watched Wes ride away, furious. Wes was actually pleased with his handiwork but he wasn't done. He activated the remote again detonating the second set of bombs that he put on the giant Snag Machine. The blast destroyed the base and Wes rode away leaving Team Snagem behind.

Finally free of Team Snagem, Wes made his way to the nearby Outskirt Stand. Made out of an unusable steam train, Wes ran into two men with something in the back of their truck. He paid them no mind and went in. Inside the stand, someone told him about a city called Phenac City that was just west of the Outskirt Stand. It was better than just staying here so Wes headed there. At the entrance were the two men with the bag in the back of their truck that Wes saw at the Outskirt Stand. They were moving what appeared to be a heavy bad out of the truck. However, Wes noticed something wrong. The bag was squirming and sounds from a gagged mouth could be heard. Wes defeated one of the two thugs, whose name was Folly and he and his buddy Trudly, and they fled, leaving their bag. Wes untied the bad and it turns out that inside the bag was redheaded girl by the name of Rui.

Rui was lost and alone and she was scared that the Folly and Trudly would come after her again. Wes reluctantly agreed to help her. Not knowing where to go to bring Rui home. The pair went to see the Mayor of Phenac City: Es Cade. The mayor said that he would begin an investigation to stop thugs like the pair that kidnapped Rui. He also told them to check out the Pokémon Stadium in Phenac City. On the way there, Wes ran into some of his old friends from Team Snagem. He had no idea how they followed him to Phenac City but there they were. As they talked, Rui found out Wes's real roots in Team Snagem, that Wes was one of the best Snaggers in Team Snagem, and how he betrayed them. Wes was getting sick and tired of this so he defeated his old pal, Wakin. After the battle, Rui had the idea to go and buy some Pokéballs. After searching around for some, Wes and Rui got some, free at the Outskirt Stand.

When the pair got back to Phenac, They heard from the townspeople that Mayor Es Cade was in trouble. They ran up to the mayor's office to find, not the mayor, but Folly and Trudly, three men dressed in futuristic armor, and a tall person in a sparkly gold disco outfit and afro hair painted half red and half white to look like a Pokéball. His name was Miror B. Miror B. couldn't stay though. He left the mayor's office with his three men in uniform to leave Folly and Trudly to battle Wes. Wes easily beat Folly but then Trudly was up. He defeated his first two Pokémon with ease, but when Trudly sent out his Makuhita, things got weird. Rui looked at Makuhita and saw a black aura coming off the Pokémon. Rui remembered. That was why the thugs kidnapped her, because she can see those Pokémon. Once Wes heard this, he knew what he had to do. He looked at his left arm as saw the Snag Machine. He took one of the Pokéballs that he had and used the Snag Machine to turn it into a Snag Ball. He used it to successfully snag Makuhita.

Wes and Rui then left the mayor's office to meet the three men in different colored armor. They were blocking the exits of the city. Wes defeated them and after learning that they artificially shut the Pokémon's heart off, headed for Pyrite Town, where Rui was kidnapped.

At Pyrite Town, Wes and Rui wandered through the dry, creepy town and met an influential man in Pyrite, Duking who informed the couple that in Pyrite, Shadow Pokémon were openly offered to winners of the town's Colosseum tournament. The local police force was powerless to stop the practice, so Duking, asked Wes to enter the tournament and investigate. Wes then found himself at the Pyrite Stadium where he won the tournament. As he left the Colloseum, Wes was stopped my a man in armor similar to that of the worn by Miror B.'s minions. He led Wes and Rui inside a nearby building where a Cipher Peon was about to present the Shadow Pokémon prize, but another one recognized Wes. The pair then battled their way through the building went into a maze-like cave set in the rock wall behind the building. As they battled through the cave, they eventually make their way to the disco-loving mastermind behind the Shadow Pokémon operation in Pyrite: Miror B. After defeating him and his four Ludicolos and snagging his Shadow Sudowudo, Wes returned a Plusle, the Pokémon Miror B. stole from Duking. After being thanked by Duking, a team of kids working in Duking's house introduce themselves as members of an anti-Cipher news network, known as the Kids Grid, who pledge their help to Wes and Rui.

As Wes and Rui are about to leave Pyrite, they are stopped by the town's fortune teller. She informs the two heroes that their next stop is Agate Village, a forested village in the mountains. This happened to be the place that Rui was on her way to when Folly and Trudly kidnapped her in Pyrite Town. Upon arrival, Rui introduces Wes to her grandfather, Eagun, the elder of the town. However they are interrupted by another villager runs into the room, telling them that the Relic Stone is under attack. Wes, following Eagun to the center of the tree, fights off four Cipher agents and enters the vast mystical space. Cipher knew that this stone was the only method in existence for purifying Shadow Pokémon and they sent their agent to destroy it. Eagun wouldn't let it happen so he challenged the Cipher Commander. After Wes watched Eagun and his loyal Pikachu lose to the Cipher Commander and his Shadow Hipmontop, Wes challenged him, snagged his Shadow Pokémon and secured the safety of the Relic Stone. After resting, Wes was given access to the Relic Stone, the only place where he can purify Shadow Pokémon. On a suggestion from Eagun, Wes decides to train his skills at the nearby Mt. Battle.

Upon reaching Mt. Battle, people informed Wes and Rui that Cipher has already taken over the first section of the mountain. After battling nine other Trainers, Wes battled the Cipher Admin, Dakim. Dakim owned a Shadow Entei.

After defeating Dakim, Wes learned of a secret town under Pyrite, known conveniently as The Under. Unfortunately, The Under was already run by Cipher and everyone there looked up to a beautiful woman by the name of Lady Venus. Luckily for Wes, and Rui, more members of the Kids Grid were there. They told Wes of Venus who was actually another Cipher Admin and she has great influence over The Under. After Wes confronted Venus and snagged her Suicune, Venus fled with Wes in pursuit. Her plan of escape was an underground subway that headed to an undisclosed location. After finding the key, that Lady Venus dropped, the heroes headed to Shadow Pokémon Lab via the subway. It was here where Pokémon were transformed into Shadow Pokémon. Unfortunately, when Wes left the subway a Cipher trainer saw him. He ran away. He knew he had to stop Wes from entering the lab. Unfortunately, in his panic, he dropped the key for the front door. He knew what he had to do. He set a bomb in the middle of the room, stepped back and blew it up. This created a chasm in the floor, making it impossible for Wes to enter. He was pretty pleased with himself and walked away, laughing. After he left, Wes found a sparkle in the corner of the room. It was the key for the front door. He smiled to himself and took the subway back to The Under. When Wes got into the Shadow Pokémon Lab, he battled his way, defeating many trainers and confronting the main scientist behind this entire Shadow Pokémon plot, Ein. Wes snagged his Raikou and halted the production of Shadow Pokémon.

Wes and Rui then received word that what was previously the construction site is now complete and officially named Realgam Tower. It was designed to be the final destination for all professional league trainers in Orre. However, it was also secretly, Cipher's main base of operations. When Wes and Rui entered the incredible structure, they remet all four admins: Miror B., Dakim, Venus, and Ein. They were there and ready to face Wes again. After defeating them, Wes was granted access to the Colosseum at the top of the building. There, he was greeted by a large crowd. A Cipher man named Nascour told Wes that he will have to face four trainers. After Wes defeated all four trainers, Nascour challenged him. Once defeated, Nascour tried to leave, only to be interrupted by Es Cade. Es Cade reveals that he is really none other than Evice, the head of Cipher, and he challenged Wes to a battle. Evice and his Tyranitar were powerful, they they weren't enough for Wes and his pair of Espeon and Umbreon. When Wes defeated him, Evice attempted to escape by helicopter, but his escape was thwarted by the legendary Pokémon Ho-Oh who swooped in and blasted the helicopter out of the sky. Evice and Nascour were then arrested and the Shadow Pokémon plot was ended.

000

Or at least it was. The Orre region enjoyed five years of peace until the plot of the Shadow Pokemon came back. It all started with a young boy named Michael. He lived in the northwest region of Orre, in the PokéTransfer Lab. The head of the lab and his mother's boss, Professor Krane was studying the research of Ein on Shadow Pokémon. Why? A couple weeks ago, he had a dream were Celebi spoke to him. The fairy-like Pokémon informed Krane that the Shadow Pokémon threat would return. Since then he has been studying the Ein Files to create his own Snag Machine. One day, Krane shows Michael the Snag Machine and asks him to test it, since Krane was no trainer. However, just before he could test it, Krane was kidnapped. Three men in white armor showed up and dragged the Professor away from the lab. Michael tries to stop them but is held up by one of the men who used a Shadow Teddiursa. What a better time to test the Snag Machine? Michael snags it with ease. Unfortunately the villains, who are not identified as the new Cipher, got away.

Shortly after this, Michael goes after the Cipher Agents to rescue Krane and rescues him from the Cipher Admin, Loverina. After Krane is saved the labs now Pokémon purification system is fully operational. Michael could now purify Pokémon with ease now. With the new threat of cipher retunring to the world, Michael goes all over Orre on many adventures. He goes to the oasis city of Phenac only to discover that the entire city is being held hostage and all the "citizens" are really Cipher agents in disguise. After defeating all of them, Michael goes to the Coloseum to defeat the man behind all this, Cipher Admin Snattle. After Michael's victory and more encounters with Cipher and even Team Snagem, he learns of the Shadow Pokémon Factory. He heads right there to take down the factory. After Michael blows up the Shadow Machine at the top of the building, the last Cipher Admin, Gorigan comes out. After his defeat to Michael, Michael learns of the head master behind the Shadow Pokémon plan and the resurrection of Cipher, Master Greevil who Michael met earlier however Greevil was using the alias of Mr. Verich, who helped Michael out earlier. Greevil congratulates Michael on his progress and challenges him to come to Citadark Isle where he currently is. Michael accepts figures out how to get to Citadark Isle. It is an island off the coast of Gateon Port and it is surrounded by heavy storms and harsh whirlpools. Luckily, Michael used an advanced speed boat called the Robo Kyorge. With it Michael arrives on Citadark Isle. There he fights his way through the three Cipher Admins in addition to countless Cipher agents. Michael finally arrives at the top of the island which is an enormous dome. Greevil is waiting for Michael when he arrives. Greevil laughs manically and reveals to Michael, his most powerful Shadow Pokémon, XD-001. A hole in the dome opens up and an enormous Pokémon enters through. Michael recognized it as the legendary Pokémon of the sea, Lugia, however its skin was purple, not white, and its eyes were red. Michael used the Masterball which he got from Professor Krane to successfully snag Shadow Lugia. Michael then snags the rest of Greevil's team. After the battle, Greevil prepares to blow up Citadark Isle and everything on it, including Michael. However, his plans for evil are halted when his son enters and begs his father to stop. The words of his son get through to Greevil and he halts his evil ways.

In the months following, Michael spends his time purifying all 83 Shadow Pokémon, including Lugia who was said to be impossible to purify. The threat to Orre finally gone for good, Michael released all the Pokémon that he snagged and caught, all except his loyal Jolteon that evolved from the Eevee that he had. With nothing left to worry about, and with all the Shadow Pokémon purified, Michael returned home and retired his snag machine, but he leaves it safely on the table in the lab, ready to be used if it is ever needed again. Little did he know that he would be needing it again.

Sorry, this is kinda lengthy. I had a lot I wanted to get in before the official story starts. Please Like and review. Thanks ;)