A/N: First off, the reason why I didn't mention Gold and Blue is because, a) I only own the Silver version and I like Silver as a name more than Gold, b) my husband owns Crystal so I'm using the girl character from it as Silver's sister, c) Blue goes by the name Gary and will appear when the gang reaches Kanto, d) Red himself doesn't appear until after Silver makes an appearance in the Johto part of the story due to the fact that he was in Johto when Cipher starts the invasion.

Due to the fact that I'll be needing to hunt down my old Johto and Kanto notes for this, expect the sequel to be slower going than Pokémon Colosseum: Apparitions. Also, you may need to read Apparitions to fully understand this story, as it follows the first story almost directly. But then, that's why I have the prologue, to help you readers out and give you a basic rundown of what to expect.

Now, Pokemon and all things associated with it are property of Nintendo and Game Freak, those lucky, lucky bastards. Sera Evice is my idea, that evil twisted woman! Jupiter and Pluto are also mine, I raised them from babies in Silver to be my best Pokémon and used the names in Colosseum to grant respectful memory to them. (my game got corrupted, don't ask how I did it, but I've got 15 bikes in my backpack. -;;;)

On with the story!


Prologue

The land of Orre had been under the domination of the criminal syndicate called Cipher. With Team Snagem under its command, dozens of Pokémon were stolen from trainers, made into fighting machines by artificially closing their hearts, then used to overtake colosseums and cities. Slowly, Cipher began to branch out to take over the world.

But as they began to move in on other lands, positioning themselves for takeover, one young man dared to interfere. Seth, also known as Wes and Project: WSLY, escaped Cipher's control and fled Team Snagem, taking with him the only portable Snag Machine left in the hideout before blowing it apart. Cipher and Snagem wanted revenge for this fact.

In making an attempt to disappear into the desert, Seth found himself coming to the aid of a young lady named Rui Roane from Zirconia City, far south of Pyrite Town. Rui possessed the unique ability to see Shadow Pokémon, the creations of Cipher, and became a prisoner of Cipher until Seth rescued her. The two joined forces to snag all the Shadow Pokémon Cipher created, purify them, and stop the organization's evil plans.

They succeeded and the mayor of Phenac City, Es Cade, was arrested with his underling, Nascour, upon discovery that he was the Cipher Head, Evice. Cipher and Team Snagem had been disbanded. Or so everyone thought.

Evice's daughter, Sera, made the attempt to rebuild in Orre her father's fallen corporation, using data hidden within Seth's own mind. Using another experimental Pokémon-gone-wrong, Cipher's new Admins captured Seth and extracted the information they needed. Rui followed to save him and, in the process, discovered Seth's origins.

Sera's DNA had been used as part of the experiment used to create Seth, effectively making him a partial clone of the corporate woman. The DNA of Groudon and Kyogre, two legendary Pokémon, were also used. The combined DNA produced an enhanced human that could seek out powerful Pokémon, withstand environmental climates to certain extremes, and store vast amounts of data in its brain, Seth.

The rescue ended in tragedy with the shadow beast killing Seth as they escaped the Shadow Pokémon Laboratory. For all of his deeds in efforts to redeem himself, Seth was granted a second chance by Celebi, the time-travel Pokémon.

One month after Seth was revived, Nett discovered through the data he had stolen back from Cipher that the organization had its roots set in the other lands and were ready to begin their final motions to conquer the world. While the Kids Grid Network attempts to make contact with the other lands to find out their situations regarding any unusual Pokémon and trainers, Seth and Rui must return to their traveling ways and stop Cipher before everything they know is destroyed by their evil influence.


Ch 1

Rui shook Seth's shoulder, trying to get him up. In her hand was his PDA, the most recent e-mail open on the screen. The urgency of the mail was evident by the fact that everything had been written with a red font.

"Seth! Wake up!" she called to him. He frowned in his sleep and rolled over, slapping her hand away as he pulled the blankets over his head.

"Mmmgh..." he mumbled under his breath. Rui set the PDA down and yanked the covers from him. "Hey!" Seth sat up and rubbed at one eye, glaring up at her, "What's your problem?"

"Nett sent us an e-mail! He made contact with the professors!" she cried excitedly. Seth stared at her blankly. "The ones from the other lands! Hoenn and Johto and Kanto! He got responses from all three of them!"

"So?" the Snagger muttered, getting out of bed and stretching. The two were in a hotel in Pyrite Town, making their way to Agate from a trip to Zirconia City. Rui had told her parents that she was going on a trip with her new 'boyfriend', at which the couple yanked Seth into the house and grilled him on rules and regulations on how to treat and act around her. He was able to sway them by showing his training skills on their pet Meowth. The cat had taken to disobeying them for almost no reason. Seth sat before it and, with the help of his Eons, finally managed to calm it down and understand the problem. It was in heat. While Rui's parents whisked it off to a Day Care Center in hopes of breeding it, she and Seth made a run for Pyrite.

"There's big trouble in all three lands! Strange teams that the people have never encountered before are attacking Pokémon Gyms and trainers everywhere!" Rui exclaimed, "Nett says that the professors say that it's getting worse day by day!" Seth nodded to himself, thinking about it as he picked up his jacket from the chair he had tossed it on the night before. "According to the mail, Professor Birch of the land of Hoenn reports the worst conditions over there. Profs. Elm and Oak of Johto and Kanto say that they are able to fight off the attacks, but they aren't doing too well. They need a way to fight back against the Shadow Pokémon being used against them!"

"So, Hoenn is taking the most casualties in Pokémon and trainers?" Seth asked, buckling the jacket, then fitting the Snag Machine onto his arm. Jupiter and Pluto, his Espeon and Umbreon, rubbed against his legs, yipping for food. "Wait a sec, guys. I'm not done."

"Yeah, but there's no real knowledge as to why Cipher's doing all that. I mean, they stole Pokémon and made them Shadow here, why not just do that over there? There's lots more Pokémon in the other lands than here in Orre." Rui answered, watching him pull his boots on and fasten the straps around them.

"Not sure. Give me a sec." Seth replied and closed his eyes, tilting his head back. It was an exercise he had begun to recall data that had been stored in his mind by Cipher. It didn't always work and most of what he was able to recall were usually snippets of information that were barely enough to tell him anything. "Uhh..." he groaned softly, head beginning to ache from the concentration effort, "It's asking for something... a pass-code of some kind. Tell Nett that the information about their plans are protected. He's going to have to crack that code."

"Anything else?"

"Mmm... a note. A note about me. Dated sometime around the day I blew up the hideout, maybe earlier." He opened his eyes and rubbed his temples with both hands, wincing in pain. "That's all I can get. He doesn't have much to work with from that, but I'm sure he'll manage." Rui sent the mail off and they got up to check out of the hotel, resuming their journey north.


They hadn't gotten very far from Pyrite when the PDA rang. Rui pulled it from Seth's pocket as he continued driving the speeder and opened it. She skimmed the mail and tugged on Seth's coat-tail. He pulled over and looked back at her in irritation, he had been making good time and didn't like stopping, the freedom of racing around was too much fun for him though he'd never admit it to anyone.

"He's got the file on the plan but says it will take a while to crack the pass-code on it." Rui told him, pointing at the mail. She looked horrified, "But Professor Birch contacted him again! Hoenn is under siege! Every city is being attacked by Team Venus!"

"Team... what?" Seth asked, lifting the visor and raising an eyebrow at her. His mouth twitched as she repeated the name. Rui jerked in surprise as he threw back his head and laughed, body shaking from the motions.

"Seth! Take this seriously! Stop laughing! Prof. Birch has sent transportation to the northern shore to pick us up and take us to Hoenn! Now stop that and let's go!" she demanded as he hunched over the fuel tank of the speeder, hiding his face in his arms while he continued to laugh.

"Team... Venus? By the fires of Ho-Oh, who the hell thought that up?" he finally managed to get out and spent the next hour with his turtle-neck collar pulled up over his mouth, protecting him from the sand as he drove and laughed at the same time.


The northern shoreline was where the land of Orre met with the ocean. The drive there was long and tiring for the two, who had alternated between each other in order to reach the sea within the two days that Nett had reported their transportation would arrive.

Rui pulled up to a small sea-plane that stood waiting for them at the shore. Dismounting, she looked over at Seth, who slept in the side car after overexerting himself at the controls to let her sleep longer. Nudging him awake, she waited for the pilot of the plane to come up to her.

"Hi, uh, you two are the ones Professor Birch and Nett were talking about, right?" he asked, "Rui and Wes?"

"Seth, actually." Rui corrected tiredly, "He's just known as Wes sometimes. It's a long story."

"And one he doesn't need to hear." Seth muttered as he sat up and stretched again. He looked at the plane after getting to his feet and went pale. "No. I'm not getting in that." he murmured, shaking his head.

"What's the matter? Scared to fly?" the pilot asked with a slight smile, "Don't worry! I'm the best pilot Birch knows and I guarantee you'll make it to Hoenn in one piece!" He waved them over as he jogged back to the plane, "You'll have to leave that bike behind, though! My bird can't handle its weight! Sorry!" Rui twined her fingers into Seth's hand and looked up at him with a smile.

"Don't be afraid. I'll be there with you, like always. Now, let's grab our stuff and get on." she whispered. Seth swallowed and picked out his pack, slinging it over his shoulder as she followed him to the plane.

The interior of the plane was cozy and Seth planted himself in the first seat he found, stuffing his pack under his chair. Rui slung hers in the overhead compartment and sat beside him, grinning with excitement as she buckled her safety belt.

"This is gonna be sooo cool!" she squealed as the pilot announced their departure and revved the plane up. Seth shut his eyes and gripped the armrests as it skimmed along the ocean surface, picking up speed and finally taking off.

"Yeah, listen, I'm just going to sleep this whole trip away. Wake me when we touch land again." he growled and promptly began to count Mareep in his head. Rui rolled her eyes and gazed out the window, counting the stars and squealing at the groups of water Pokémon that swam the vast blue ocean.


Seth woke with a start upon the plane's landing roughly. Rui was clutching him, eyes wide as the pilot declared that they were experiencing 'technical difficulties'. Struggling to get free of both Rui and his seat-belt, he grumbled angrily and finally got loose, lurching forward on the plane as it rattled.

"Yeah right, stinking liar." he growled and kicked open the door, throwing out the Poké Balls containing the twin Eons, "Jupiter! Pluto! Prepare for battle!" A pair of women just outside jumped back in surprise, their Pokémon unleashing attacks on the plane. Seth took them in quickly, recognized them as Cipher Peons from the way they were dressed, and set the Eons after the Ninetails and Manetric that attacked them.

"Eeks! It's that guy Lady Venus was talking about!" one woman cried and pulled her Pokémon back, "I'm out of here! I don't want my Ninetails getting snagged!"

"Wait for me!" the other cried, following her partner's lead. Both of them fled the scene before either Eon could make a move. Frowning, Seth returned to the plane's interior to grab his things and help Rui outside.

In the span of a few minutes, people were emerging from their homes, running up to the plane as they stepped down the ladder to dry ground. One of them bustled past the group and stood before them, panting. He was a rather large man, wearing khaki shorts and a dark blue shirt under his lab coat. He was bearded and would have looked friendly if he hadn't been wheezing.

"Thank... goodness... you... made it!" he gasped and ran his hand through his hair, wiped it on his coat and held it out to Seth for a handshake, "I'm Professor Birch! Welcome to Littleroot Town!" Seth glanced at the hand, then at him, silent. "Uh, nice to meet you both?" the man went on, holding it out to Rui, who shook it tentatively. "Um, well. Sorry for the rude welcome from those two back there. We've been having trouble like that for a couple of weeks now. Team Venus has taken over five of our eight official Pokémon League Gyms and I told Professor Nett this. He said that you two were experts in dealing with teams like this so could you help us out?" he asked pleadingly.

"What the hell is a Gym?" Seth asked, brows furrowed in frustrated confusion as Rui raised her own and mouthed out the words 'Professor Nett' in surprise, "And who said anything about Nett being a professor? He's just a kid!"

"Oh? I just assumed it... anyway! A Gym is a building authorized by the League to award badges to trainers who defeat the leaders as part of their training to compete in the Ever Grande Challenge. You need eight badges to gain admittance to the challenge and entry to the Elite Four's arenas." Birch replied, "But that's beside the point. It's like a war out there! Trainers from all over Hoenn are trying to fight back against this Team Venus and we're losing badly!"

"They must be using Shadow Pokémon to overthrow the Gyms. Seth! We have to find them and Snag them!" Rui exclaimed. She turned to the professor. "Prof. Birch, do you have a map of Hoenn we can use?" The man blinked and dug into his pockets.

"Um, I have something here to help. Ah!" he cried, pulling forth a small red device. It opened like a tiny laptop, revealing a screen and several buttons. "This is a Pokémon Navigator, PokéNav for short. It contains a map as well as various other features. You can use it to get around the place, but you have to get to Petalburg City first and foremost!" Seth took the device and handed it to Rui.

"Why?" he asked.

"My son is out there, fighting alongside the trainers from that city. I have to know if he's safe. I lost contact with him shortly before you arrived. Please, go there and help him! Help him and Norman Thorne's daughter escape Petalburg!" Professor Birch pleaded.

"Don't worry! We'll take it from here!" Rui cried as she and Seth began to run off, following the map to Petalburg. "We can handle anything Cipher throws our way!"

"Look for Brendan and May! They're the ones you have to find!" Birch called out and sighed, then looked perplexed. "Cipher? Isn't that the corporation that's been trying to merge with the Devon Corporation? I'd better call Professor Elm and Professor Oak about this."


"How much further to Petalburg?" Seth called back as they ran up the road, mentally cursing the pilot for making them leave the speeder behind. Rui checked the Nav quickly.

"Up ahead is Oldale Town! From there we use the Route 102 to reach Petalburg City!" she called ahead, "Judging by the scale of the map, I think it's about thirty miles away!"

"Not as the Murkrow flies!" Seth declared and dashed into the forest beside the road, "Come on! We'll cut through the woods and head straight there!" Even though it was late at night, the sky seemed almost bright as day with flashes of light erupting everywhere. Whatever was going on, it was tearing Hoenn apart.