Hello everyone! I'm pretty new to the whole Fanfiction thing, and this is my first story of decent length. To be up front, this story is set in an AU of Pokemon Special and there will be 4 OCs added to the main cast of characters.

Disclaimer: I do not own Pokémon.

Chapter 1: Vs Rumors

Crystal smiled as she sifted through the data that appeared on her computer monitor, "Good work guys!" she said. "This is really good data! How long were you able to observe this Heatran for?

"About three minutes," replied Pearl with a smirk through the monitor. "It eventually noticed us and moved into the caves and we lost it, though."

"Indeed," said Platinum. "We have completed almost 98% of the pokedex. We were wondering where we should go to observe a Porygon Z – it's very hard to find to our understanding."

"Don't worry about the Porygon Z" said Crystal, "Just focus on Shaymin and Manaphy for now. I know someone with a Porygon Z, but he's not easy to get ahold of." Crystal smiled as she scanned through the files of data on the Pokémon the trio had scanned. "The Sinnoh Pokedex is coming along very well! You have no idea of how proud I am of you!"

"You're the amazing one, Senior Crystal!" said Diamond. "You're the one who singlehandedly covered all of Kanto and Johto!"

Crystal smiled awkwardly, "I had lots of help you guys. I didn't do it alone!"

"Yeah, but you did most of it, right?" asked Pearl, interested.

"Err…not exactly….." she muttered.

"What's that supposed to mean?" asked Topaz.

"Well, I just didn't do it all myself," she corrected herself hastily. "I wouldn't have been able to do it without a lot of help from a lot of a lot of people."

"That's all right!" grinned Pearl, "Don't sell yourself short, Miss Crystal!"

Crystal smiled, "Well, I'll get started on the data upload. See you later!"

"Bye Miss Crystal!" the four chorused before the connection ended.

Crystal took off her headset and smiled. The Sinnoh Pokedex was almost complete along with the Kalos and Unova Pokedexes. The Alola dexholders had gotten a later start than everyone else due to a series of bad storms that had prevented the shipment of their pokedexes, and the Hoenn group…well, the less said about the Magma and Aqua fiasco, better. She leaned back in her chair at her workstation. It was remarkably neat compared to the messy workstations next to her, a testament to her meticulous organizational habits. Her musings were broken with a knock from the door behind her. Turning around, she saw Professor Oak, with a grave look on his face.

"Crystal, I'm afraid I have bad news…..please, come with me."

Crystal stood up from her chair. "What's going on professor?" she asked, as they walked down the short hall to the break room. She paused in the doorway, "Professor?"

Sitting around one of the tables were Brock, Misty, Erika, and Blaine, with varying expressions ranging from grave to worried. Professor Oak pulled out a chair and sat down. "Please, sit down. What we are going to talk about here will not leave this room. Is that ok?" Crystal sat down, nodding.

"The Pokedex Project has been shut down. Again," said Professor Oak.

"What? Again?" asked Crystal in shock. "Why?"

"We're sending kids into danger. You know, what they said last time," said Oak.

"We aren't sending them into danger!" protested Crystal. "They chose to fight the evil teams on their own! We chose to fight evil teams on our own! We specifically told them not to go! Didn't you send them copies of the many messages we sent telling them NOT to go!?

"Yes, I did. The Chairman was adamant. 'Your program, as well intentioned as it is, has a history of sending children into danger!'" the professor groused as he impersonated the voice of the Chairman.

"Ever since the Magma and Aqua debacle, people have been asking a lot of questions. I still don't know what Ruby was thinking when he joined Team Magma and what Sapphire was thinking when she joined Team Aqua! If they weren't so instrumental in bringing them down, Birch and I'd be in a whole lot more hot water! Then, there's the recent revelation that Whitley was formerly part of Team Plasma. That isn't helping either. I don't blame the poor girl, but I know that the league council hasn't seen it so favorably. I'm just thankful that your generation of dexholders hasn't come under much scrutiny - I've been spending more time placating regulatory officials than I have on my research!"

"But that's not all," said Erika, taking over for the frustrated professor. "I'm sure you've heard of the rumors about Team Rocket."

"The rumors that Team Rocket has returned and is controlling the Pokémon League? I have," said Crystal, "You think that there's merit to that?"

"We do indeed," said Erika. There was an uncomfortable silence.

Crystal asked tentatively, "What makes you think that?"

Brock pulled out a folder and opened it for Crystal to see, "We've had a 450% increase in rare and strong Pokémon reported missing that has held consistent for the last two months in Pewter City."

"We've had a 370% increase for the same time," said Misty, pulling out a folder of her own. "The other Gym Leaders have been reporting similar rates as well."

"This is clearly not a coincidence. Combined with several reported sightings of Team Rocket in numerous locations around Kanto, there is no doubt in my mind that Team Rocket has returned," concluded Blaine. "The only question is what we're going to do about it."

"So, what are you thinking?" asked Crystal cautiously. "Are you going to be investigating?"

"We cannot," said Blaine with a hint of defeat in his voice. "All of us Gym Leaders are too public. We're very likely being watched. Furthermore, it would be catastrophic if confirmation that Team Rocket returned went public. Panic would reign supreme!"

"We also can't abandon our Gyms and cities to go on wild goose chases," said Misty. "We need concrete evidence before we act."

"You need evidence…. You're going to recall the dexholders – the original ones?" asked Crystal hopefully.

"That's…well, we are, to some extent," said Professor Oak. "Of course, the existence an original Pokedex Project, made up of a roster of currently well-known figures from Kanto and Johto is technically just urban legend. You know, because of the League. I'm sure Team Rocket hasn't forgotten how you took them down the last three times, though. It's not a total recall at the moment. Since we have some dexholders that are square in the spotlight and some dexholders that are relatively unknown, we have a unique position. Some of you are integral parts of the League and can act as best they can there. However, you and some of the others are out of the public spotlight and can operate behind the scenes. The only question is, are you are willing to do this?"

"I'm in," said Crystal quickly.

All present looked at her strangely.

"What?"

"Well, I guess we weren't expecting you to agree so quickly. You've adjusted well to your position here at my lab and we weren't sure if you were willing to get back into the field again," said Professor Oak with a smile.

"Have you talked to any of the others?" asked Crystal.

Professor Oak leaned back in his chair. "I've already talked to Red and Green. They are both solidly in the public eye being the Champion and the strongest gym leader of Kanto respectively, and they are almost certainly being watched. We've talked it over, and they're investigating as best they can behind the scenes. However, we won't be able to expect any help from them at the moment."

Crystal nodded.

"Blue, and by extension Silver, are both in Kalos. As I'm sure you've heard, Blue is doing filming for that new Pokebot Wars movie. She said that filming will finish tomorrow, and she can be back the day after that. They will join us then. Fortunately, Violet is in Johto, and Indigo and Lyra are supposed to come home tomorrow from their trip to Orre. I have already contacted them, and they will join us tomorrow."

"Did the tweaks to the purification machine work?" asked Misty curiously.

Professor Oak sighed, "It didn't. It fried some of the circuitry. Apparently, Indigo wasn't updated on all the other changes they made, and something didn't mesh well. Thankfully, they didn't get far enough in the trial runs to try it on one of the Shadow Pokémon."

"That's a relief," said Crystal.

"Yes, it is," Said Professor Oak. "I'm just glad he's able to make it back so quickly. Lyra seemed pretty keen on getting here too."

Crystal nodded. Having one of the "sibling" duos with her would be invaluable.

Erika asked, "What is Violet doing in Johto?"

"She's out by the Whirl Islands helping a group of Pokémon Rangers with a pod of Lapras. Apparently, they've had a several run ins with poachers," replied Professor Oak.

Everybody winced in sympathy.

"Has she….." started Misty, but Blaine cut her off, "Misty. This is Violet we're talking about. I may as well order the hearing aids for the poachers already."

Everyone chuckled. Brock asked, "Professor, what about Yellow and Orange? Can't we call on them?"

The professor sighed and said "Yellow and Orange are missing. They are actually the reason I'm trying to get the old dexholders back together again."

"What!?" gasped Crystal. "Wait – isn't Orange usually missing?"

"She hasn't checked in with anyone for the last three weeks," said Professor Oak.

"W-where was she last?" asked Crystal. It was a well-known fact that the independent dexholder would sometimes just drop off the face of the earth as she wandered wherever the wind took her, but she almost never outright disappeared for more than a few weeks in succession.

"North of Pewter, in the mountains. She went off to investigate the Team Rocket rumors – she said that someone had told her there was a base in the area. You remember my conversation with her a few weeks ago?"

Crystal nodded. The professor had been on the phone for nearly an hour – a rare occurrence for the aging man.

"I asked Yellow to go with her because I thought they'd be safer together, and I haven't heard from the two since. I hope….I just hope I haven't ….." the Professor trailed off.

Crystal sat up straight, "I'll go, Professor."

"No!" said Oak sharply, "I'm not sending you in alone. Not after what just happened. I wasn't going to say anything about it until the others got here so you wouldn't just go off on your own. You're going to wait for the others to get here," He stopped himself abruptly.

"I'm sorry – I don't want to be pushy or rude. I just don't want to be sending more of you into danger. You're all like my grandchildren to me." He took a deep breath. "I'm just worried for them and for you."

"It's all right. Is there anything I can do while we wait for the others to arrive?

There was a pause, and Professor Oak looked a bit uncomfortable. Crystal knew exactly what he was going to say.

"No, I'm not going to get Gold."

"He is a dexholder…"

"No. Not after what happened. I'm sorry, I don't think I should be the one who goes to get him. I'll work with him, but I'm not going to talk to him," said Crystal firmly.

"Well, it was worth a shot," said the professor sadly. He ran his hand through his hair and took a long sip of his coffee. "I can't think of anything. Just make sure you're ready for tomorrow."

"I can do that," said Crystal.

"Thank you, Crystal," said Professor Oak, gratefully.

Blaine rose to his feet.

"Unfortunately, we need to get moving. We can only leave our gyms for so long and we're officially here to inspect the lab itself on behalf of the league, and we haven't seen head or tail of the lab yet. I apologize Sam, but we do have to do our jobs," he said towards Professor Oak.

"It's no problem, Blaine. Like you said, you're just doing your job, and I have nothing to hide," said the professor.

"We'll keep an eye out and let you know if we find anything out!" said Misty as she rose to her feet along with the other Gym Leaders.

Crystal waved as they filed out.

Professor Oak rose to take the gym leaders into the lab, but paused for a moment.

"Crystal…thank you. I realize that its asking a lot to be meddling with Team Rocket again, but…."

Crystal smiled wryly.

"We're dexholders, Professor. Getting into trouble is what we do best."

Dexholder Manual:

In the event that the pokedex project is taken over by another leader, I have resolved to write explanations for decisions made in the program and profiles for all existing dexholders to help smooth such a transition. These will be updated as frequently as possible.

Professor Samuel Oak, PhD

Dexholder Profile: Crystal

Title: The Capturer

Crystal is a strong trainer and invaluable lab assistant who will doubtlessly become an esteemed Pokémon Professor in her own right. She is a grounded, serious and direct person with a tremendous talent for capturing Pokémon. After having broken her arms on Mt. Mortar as a child, she learned how to kick pokeballs with greater accuracy than throwing them by hand. She has also worked many years at Earl's Home for Children, an orphanage in her hometown Violet City, and has become an inspiration to all of the children. She has performed the role of Lab Assistant to an admirable extent and has worked with me in the revived Pokedex Project. She is the only member of the Senior Dexholder generation to have met all members of the Junior Dexholder generation. Crystal's greatest shortcoming is that she is known to be very conservative and follows the rules closely, even to her detriment. This does limit her flexibility, but also means that she'll keep her allies on the straight and narrow. Additionally, she has had a severe falling out with Gold, and it is wise to have the two interact as little as possible for the foreseeable future. She works in best in conjunction with Silver, Lyra, Yellow and Red.

Team:

Meganium (Mega)

Smeargle (Smeargee)

Fortress (Fortee)

Venusaur (Venee)

Noctowl (Noctee)

Sudowoodo (Sudee)

Note: In case of any confusion, Topaz is an OC that will not play a major role. Orange, Indigo, Violet and Lyra will all play major roles. Dexholder Profiles will be attached to the end of chapters in which new Dexholders appear in the story, as I've made some tweaking to backstories and teams. Other short paragraphs from the Dexholder Manual by Professor Oak will also appear to explain other changed plot points.