Anguirus111 Note: Confused? Yeah you should be. This story begins heavily in medias res which means there is a lot you don't know. If you've followed some of the other The Legend stories, this is the sequel to The Pokemon Conspiracies. Yes I know I didn't finish that story and likely never will, but this story both fills in the gaps of that story(proves why it was a conspiracy surrounding pokemon) while also discussing a prequel story to The Pokemon Conspiracies that I didn't write yet. Hopefully it'll all make sense as the story goes on and if it doesn't I'm sorry. But hey, it is a mystery right?

War Cabinet, Location Undisclosed: A group of generals from Kanto, Johto, Hoenn, Orre, and various other regions filed into the darkened room that was equipped with only a single long table and various displays all around it. As they entered and took their seats, the PM was already standing up at the end of the table looking very unkempt with his jacket unbuttoned, his tie hanging loose around his neck, and his hair going in several different directions.

"Is everybody here?" he asked. "Okay let's get started."

"Shouldn't we wait for The Legend?" asked one of the generals named Sherman.

"To hell with The Legend," grumbled an older general named Taggart who was busy smoking a cigar. "If it were up to me we'd have hunted him down and destroyed him long ago. Good riddance to bad rubbish I say. He's a security threat, nothing more and nothing less."

"Unfortunately Taggart he's already here to have heard you say that," said a voice from the shadows. As the group turned towards the voice, another Prime Minister, identical in image to the one currently at the table, strode in carrying a briefcase that was bulging with papers. As he strode in, he stood by the first Prime Minister and looked at him bemused.

"Uncanny," he said shaking his head. Taggart suddenly leapt out of his chair with his gun drawn as he pointed it to the two individuals.

"Alright what's going on here?" he demanded. The two PMs looked at him.

"Put that away," said the first as he threw down his arm as at the same time Taggart's arm slammed down as well.

"If you would take your seat," said the second PM to the first. The second nodded and took his seat as his image morphed from the PM to The Legend.

"Wow," said a younger general named Smith in awe. The Legend looked at him curious.

"I can see we have some new faces," he said before turning to Taggart who was scowling at him. "And some who just won't go away."

"Enough chit chat," Taggart said. "Did you find our missing warhead or not?"

"Oh I found it alright," said The Legend.

/Flash/;

The Legend and Giovanni tore down hallway after hallway inside of the Indigo Plateau as they desperately tried to elude the pursuing enemy forces intent on their destruction.

"Through there," said Giovanni pointing to a massive blast door ahead of them. "That looks promising."

The Legend, still wearing the damaged psychic equipment that had once belonged to Mewtwo, used his powers to push the massive door open as the two rushed inside only to slam it shut behind them as several pokemon slammed into it.

"That should hold them for awhile," said The Legend banging his hand on the door. As he turned around he noticed Giovanni looking at a massive tube shaped object in the center of the circular room they were now in.

"Oh my God," said The Legend in shock as he stared up at the warhead with the letters: JSDF emblazoned on the side of it.

/Flash/;

"So spill it, when in the timestream is it?" said Taggart.

"I found your warhead a good 1100 years in the future," said The Legend. The War Council erupted over that statement.

"1100 years in the future? I thought it was 6000 years in the past!" shouted Taggart over the rest.

"Quiet!" shouted the PM over everyone. There arguing went on for another couple moments before an uneasy silence descended on the group.

"Please explain," continued the PM to The Legend. The Pokemon nodded.

"As we all know sixteen months ago the security surrounding a classified project involving Verteron Particles was breached. Before anybody could react, the outcome of that project, the Verteron Warhead that was safely secured at a launch site in Orre vanished without a trace. You sent Alpha Flight in to investigate and they vanished without a trace. As that was going on Professor Eve who was investigating the remains of Pokemopolis uncovered a cave drawing depicted a very crude yet unmistakable image of that missing warhead, though how it got there we didn't know. You covered it up then called me in. I showed up, you told me what happened, I went in to investigate the disappearance of Alpha Flight and the end result of that investigation got me catapulted into the distant future where a war had erupted between mankind and the pokemon upon which I found your warhead and nearly died before traveling back here," said The Legend breathing heavily from speaking so fast. "Everybody got that?"

The Generals looked at him strangely while the PM just shook his head.

"I apologize, I didn't realize it was going to be that complicated," he said, slightly stunned.

"You think that's something, I just gave you the abridged version," said The Legend.

"Why not the full version?" accused Taggart. "Afraid we'd be too 'primitive' to understand."

"No, because someone here is a spy," said The Legend simply. The silence was so deadening that you could hear a feather drop.

"What?" asked Smith.

"I said someone here is a spy," repeated The Legend crossing his arms and leaning back in his chair. The PM sighed and dropped down onto his chair as he considered what The Legend had just said.

"How can you tell?" he asked. The Legend leaned forward in his chair.

"For the simple reason that they were stupid enough to activate a psychic suppressor to shield their thoughts while in my presence. I've got news for you buddy, it's not powerful to stop me and I've been tapping into your thoughts and it's not pretty," said The Legend looking around at the various generals.

"How so?" asked the PM. The Legend forward conspiratorially.

"Someone in this room was the one who helped arrange the little incident involving the PM this morning," responded The Legend.

"Let me guess, it was me right?" said Taggart angrily.

"Taggart as much as I would like for it to be you, you're simply too thick headed to ever turn traitor against the government," said The Legend. Taggart grumbled an expletive but otherwise remained silent.

"No, the person who did this was quite stealthy in their attempts to not be discovered but they made one mistake," The Legend continued.

"Which was?" asked the PM.

"They trusted Giovanni," said The Legend simply. "Unfortunately it never occurred to them that Giovanni would actually set them up to take the fall but I guess money clouds all judgment. So I'll make this clear and I'm only going to say it once. I don't like traitors in fact I hate them with a passion. So I leave you with a choice. You can confess now and live or you can hold onto your secret and take it to the grave because I've gleaned all the useful knowledge from you so you're no longer of any use to me. But it's your choice so go ahead, make it."

The Legend stopped talking and each of the generals all looked at each other nervously except for Taggart who just glared at The Legend. The Legend sat there for a few moments before growling angrily and standing up.

"Fine, don't say I didn't warn you Abernathy!" he shouted begin to swirl psychic energy.

"This is crazy!" shouted the general The Legend had accused, Abernathy. "Stop him! I'm not the spy!"

"I can't and I won't," responded the PM feeling unsympathetic. "You had your chance to confess and you blew it. Besides, he legally can do whatever the hell he likes so long as it's in the best interest of the government. Or so says some ancient writing we uncovered from the fifth Emperor, either way he's doing his civic duty."

"But it isn't me!" shouted Abernathy.

"You should've confessed and not decided to continue with this farce," the PM responded harshly. "I've seen the aftermath of The Legend when he's at his worse it's not pretty."

The Legend finished summoning his energy as it all coalesced into an energy ball which he promptly launched at the general. Abernathy screamed and was promptly hit with the blast full force and vanished amidst an inhuman scream. As the generals sat there shocked The Legend looked at Abernathy's chair nonplussed.

"I guess he didn't think I'd do it," responded The Legend.

"You shouldn't have that right at all!" shouted Taggart. The Legend rolled his eyes.

"You seriously want to have this conversation again?" he asked incredulously.

"We are going to have it every time we meet!" Taggart responded. "We will have it until you are finally placed in jail for genocide!"

"Genocide!" shouted Smith. "Against whom?"

"The descendants of the Pokemopolitans!" shouted Taggart. "Didn't you read the dossiers about him?"

"Sorry I haven't gotten around to it yet," responded Smith sheepishly. The Legend's eyes meanwhile began to glow dark red.

"What happens between me and the Pokemopolitans is none of your concern," he responded on a low guttural voice that scared some of the generals. "I will deal with them how and when I please and nothing you do will ever stop me!"

"Will you two give it a rest?" the PM cut in. "Right now we have bigger problems than some blood oath that affects less than one percent of the total population. Right now the entire world is at risk thanks to these missing verteron particles."

"Agreed," responded Taggart reluctantly. The Legend merely tipped his head.

"So, who has our warhead?" asked the PM finally getting the conversation on track.

"The same person who organized this little raid today," said The Legend before pointing to Abernathy's chair. "And I'm not referring to 'ashes' over there."

The PM sighed. "Great so it's Giovanni. And what possible use could a warhead like that do him? Admittedly Giovanni's goals are a bit hard to deduce at times, but he does want all the Pokemon he can get his hands on. So what does he plan to do, hold it for ransom, dismantle it, what?"

"No," said The Legend darkly. "He plans to use it."

Team Rocket HQ: Giovanni sat alone with his thoughts in silence at a massive table that was surrounded by various displays. Yet there were no other chairs at the table, Giovanni had long ago dismissed relying on others opinions to guide his own judgment and made his decisions after cold manipulative calculations. His thoughts however were now in extreme turmoil until they were briefly interrupted as Domino entered into the room.

"Any news from our source?" he asked calmly. Domino shook her head.

"Whoever this 'legend' is, he quickly disposed of our source and any link we have to the inner workings of the war council is now gone," she responded.

"Somehow I am not surprised, nothing ever seems to get by him," Giovanni commented.

/Flash/;

"Something's not right here, why would there be human remains?" asked The Legend.

"Maybe the Pokemon were torturing them?" thought Giovanni smiling as it could finally give him justification for his own torturing of Pokemon. The Legend dug up the rest of the skeleton.

"Then why aren't there any marks on this person's bones? From the looks of things, these creatures, Pokemon and human, came here and just died. But why and how?" he asked.

"You've got me. Let's just get going," said Giovanni.

/Flash/;

"So what are you planning to do?" asked Domino.

"We must accelerate our plans," said Giovanni simply. Domino looked at him like he was crazy.

"Because of one Pokemon?" she asked incredulously.

"He's not just one Pokemon, he's The Legend!" Giovanni spat at her.

"So?" said Domino unimpressed. "Everyone can be killed or bought off, you've said so yourself on numerous occasions."

"Not him," said Giovanni defeated. "And believe me I've tried. I've created traps as well as pokemon that should've been unbeatable, but he's still somehow managed to come back even after suffering sustainable injuries. And yet despite it all he doesn't consider me to be much of a threat."

"And why not?" asked Domino crossing her arms.

"Because he has bigger fish to fry," said Giovanni steepling his hands in front of his face as he leaned forward on the table deep in thought.

"And what could be bigger than the mighty Giovanni?" asked Domino disbelieving him.

"To accomplish the deaths of every single Pokemopolitan descendant that exists in the world," responded Giovanni. Domino gasped.

"That was him?" she said. Giovanni nodded.

"Yes," responded Giovanni.

"So why doesn't he just kill you like he did Abernathy?" asked Domino.

"Likely because he didn't want to be bothered with cleaning up the mess left behind by the power vacuum that would be created after my passing," suspected Giovanni. "But it's a moot point now, contact Pokemon R&D and tell them to finish whatever work they can on Blue Squad and tell them to be prepared for immediate activation. As for the Verteron Project, tell them to step up their plans, we must get those launch codes."

War Council: "Calm down!" shouted the Prime Minister again over the shouting match that had erupted after The Legend's last statement. "This is hardly a surprise; all intelligence reports have more or less come to the same conclusion. So instead of asking why, let's ask the more important question, what are we going to do about it?"

"I say we eliminate Team Rocket once and for all," said Taggart. The Legend nodded in agreement.

"And we do it now, not later," he added. If there was one thing Taggart and The Legend could agree on, it was quick decisive action against an enemy.

"Yes but the warhead is our primary concern right now," the PM pointed out.

"I'd say the launch codes are more important," said Smith. "After all, one wrong symbol and the warhead's defense measures kick in and it simply goes into meltdown, thus rendering the particles inert. The longer Giovanni doesn't have the codes the more time we have to stop him. We have to create only one copy of the codes and then destroy every other reference so Giovanni can't get his hands on them."

"So that leads to who should we give them to. We can't have the PM go into hiding with them, that could start a panic and we certainly can't give them to any of, so who?" asked Smith.

"Well whoever gets them I immediately veto The Legend from getting them," said Taggart. The Legend again nodded his head.

"I agree. I don't want your 'precious' codes, in fact I want as little to do with the government as possible," responded the pokemon.

"So now what?" asked the PM defeated.

"Hold on," said The Legend. "You're right I don't want the codes, but that doesn't mean I don't know someone whom we can give them to."

"Do you trust this person?" asked the PM.

"I didn't at first," The Legend admitted. "But he has ultimately proved himself, and given his upbringing I must say that is quite an accomplishment."

"Do I want to know who this individual is?" asked the PM.

"I don't think so," responded The Legend. "But he has no love for Giovanni I can tell you that."

"Fine," said the PM putting his briefcase on the table. He slid it over to The Legend who grabbed it and picked it up effortlessly and saluted with it.

"Alright that's enough for today. We'll reconvene tomorrow at the same time to sort out the details of taking on Team Rocket as well as give The Legend time to transfer the codes. Until then this meeting is adjourned," said the PM getting up. The Generals slowly got up from their seats and exited the room.

"Legend, can you wait for a moment," said the PM. The Legend stopped and turned to look at the PM. The PM sat there silent before sighing deeply.

"Look I'm telling you this now so we don't have any problems later on. There is a very real possibility that we will have to send you to Pokemopolis. I know of the bad blood between you and that place and quite frankly I agree with your feelings regarding that place if not so much your methods of dealing with those feelings. What I need now is your assurance that you are not going to do something stupid when you're there," said the PM. "Now is a critical juncture for the survival of this planet and I am not going to see it compromised by a grudge you can't seem to get over. If it comes down to it I won't hesitate in ordering your termination and in fact if things really turn sour I'll kill you myself is that understood?"

The Legend stood there in silence, bathed in shadow, as he considered what the PM had said.

"Very well," said The Legend darkly. "I will do everything in my power to suppress my inner demons but I won't be able to control them forever and in the end I may be more of a liability than an asset."

With that he was gone, leaving the PM alone in an uneasy silence.

Later, the Mountains of Johto: "Do you understand what I'm asking of you? These codes cannot be turned over to anyone, not even me. When the times come someone will ask you to destroy them and you must in order to preserve the future," said The Legend. He was currently inside a darkened cave with another pokemon. The other pokemon nodded.

"That's the official reasoning, what's the unofficial one?" asked the pokemon.

"If Giovanni somehow manages to take over the world I want you to use the launch codes to detonate the warhead. Yes countless millions will die, but life under Giovanni's rule would be considerably worse than death, we both know this," responded The Legend.

"I agree," said the other pokemon. "But you're going to need my help on this."

"If I need your help then memorize those codes and destroy the briefcase," responded The Legend. "I really hope it doesn't come to that, but it would be nice working with you again."

The Legend turned to leave.

"Oh, if you happen to see Mew, please send my regards. Goodbye Mewtwo," said The Legend before tearing off into the sky. Mewtwo watched him go passively.

"Goodbye Mewn and good luck," said Mewtwo before retreating back into his cave to join the rest of his clone pokemon.