Author's Notes-This has so far been a really fun project for me. I've always wanted to take a much darker, more twisted look into the mysteries of the Pokemon universe, and this fic is exactly that. It's based on both the TV series, video games, and even the more adult mangas about the Pokemon timeline, all meshed together into one story. Content is likely to get a little darker, but nothing worse than a T (although that might change down the line, who really knows? :D) Enjoy Pokemon: R for Revenge!

Prologue

Time: Unknown

Date: Unknown

Location: Silver Cave

Silver Cave-not too much is known about this mysterious cave. It houses some of the world's most powerful Pokemon, second only to the Unknown Cave in terms of the Level of the creatures housed within. The two were remarkably similar, so similar in fact that an investigation was undertaken by the members of the Rustboro Science Organization to try to find some kind of correlation between the two locations. But the two caves had one massive difference that set them apart-Silver Cave has a human inhabitant.

Just one human, among the thousands of Pokemon, but it was still a huge difference. This human had managed to get all the way to the deepest reaches of Silver Cave by himself, devoid of any tamed Pokemon to aid him.

And there, in Silver Cave's deepest room, sat that very boy-Red, the once famed Pokemon trainer. Red was sitting on a small boulder, with his chin in his hands, thinking about how far he had fallen to end up here.

How did it all begin…was it Richie? No. He was the end, but not the beginning…Team Rocket, yes that was it. Red had first stumbled on Team Rocket in Mount Moon. The were trying to steal something…moon stones? No…fossils, that was it, the Helix and Dome fossils, to recreate ruthlessly strong Pokemon. He had stopped them, and they had quickly fled. As soon as Red got out of Mount Moon, he was taken into custody by the local Police. Apparently, the Kanto Government didn't want the public to know about Team Rocket. They wanted the people to think they were just an urban myth, so that panic wouldn't spread throughout Kanto.

So he was ordered to keep silent about this, and was told that if Team Rocket struck again, he would have to come to stop them, for he was the only trainer to take them on and live.

He next found them in Celadon City, operating under the guise of a Casino. He had again defeated them, this time also taking down their leader, Giovanni. The public at large was told that the Casino had gone belly-up due to some ridiculous excuse, and the real events were covered up.

Red was getting tired at this point of keeping his exploits a secret. He knew Team Rocket was real. The Government knew Team Rocket was real. But he couldn't say a word, or he would be arrested like a common criminal.

And when Red found them again with Silph Corporation's headquarters in Saffron City taken by siege, he found that most large business owners had been informed of their existence in order to better defend themselves. Red labored for three full days to battle level after level of seemingly endless Team Rocket trainers, finally gaining the summit of the huge tower and taking out Giovanni once again. Red thought he had finally found a confident, in the form of the President of Silph Co., but he too was ordered never speak again of the events that had transpire.

Red was frustrated beyond belief. He wanted so badly to find someone to believe him, to trust in him. He wanted a friend. Red spent increasingly more time with his Pokemon than humans. They believed him, they trusted him, unlike the rest of his own race. Soon, rumors began to spread that he had lost all contact with humans. Others spread that he was going insane, thinking he could communicate with his Pokemon. Funny thing was, after all the time he spent with them, he could actually speak and understand a small amount of Pokemon dialect. That fact didn't help his image much.

Red pushed his Pokemon as hard as they could go, and farther. After almost a year spent around the realm of Kanto, he made it to the Indigo League, and there, after all that time, he found his first friend, a trainer named Richie.

Red's hands clenched into fists, and he had to force himself to calm down. Richie.

The first day of the Indigo League, Red's Pokemon were stolen from him in a last-ditch effort to keep him from ever interfering with Team Rocket again. Purely by chance, they also accidentally pick up Richie's Pokemon, thinking them to be Red's due to the Pikachu they both used.

Red and Richie retrieved their Pokemon, and together they crushed Team Rocket once and for all-or so they thought. Red was overjoyed, and he recounted in great detail his many defeats of Team Rocket with glee. Richie listened, believing every word, and sympathizing with his plight. The two were fast friends in a matter of days.

Once the Indigo League began, the two trained together day and night, both seeking to be the best, but retaining their friendship. That is, until the Fourth Round battles were drawn. Red was stunned at his matchup-we would have to face Richie.

Red took this news with a smile, however. He thought of it as a friendly test of their skills at the highest level possible, a sporting match between two friends on the big stage. Richie, however, took a different mindset. He wanted to win, and he wanted it so badly he decided he would do anything...even if it hurt Red.

The night of their battle, Team Rocket returned, tipped off by Richie where Red would be before his match. They came with everything they had left, dozens upon dozens of trainers who all attempted to keep Red from his date with destiny. Red barely managed to get out with his life, and got to his match in the nick of time by riding his Pidgeotto.

Red quickly explained the situation to Richie, showing him how beat up his Pokemon were, and how he had to have the battle postponed. He thought Richie would understand. After all, he had seen how powerful Team Rocket really was. But Richie saw his chance to make sure Red lost, and he took it.

He ran to the arena security, sobbing and blubbering, blurting out some story about how Red was demented. He told the police that he threatened him to give up, or he would make sure his Pokemon suffered. He said that his Pokemon were so exhausted because he had beaten them savagely when they couldn't perform up to his insane standards.

Red was furious. He had finally had it with all the secrecy about Team Rocket. He stormed over to the police and told them that Team Rocket had tried to kill him, and how he had fought off the villains just in time to get here.

Richie knew Team Rocket existed, but the security officer didn't.

Red recalled the fateful moment. He remembered exactly how it played out, as he had run it in his mind every day since it had happened.

The security guard looked at Richie.

"Is what he says true?' the guard asked. 'I've heard people talk about Team Rocket, and this Red guy seems serious. You're his best friend, or so it seems-is he telling the truth?'

Red looked into Richie eyes, and took a step backward. All he could see was anger, fear, and hatred.

"He's insane." Richie said evenly. "I've never even heard of Team Rocket."

Red's jaw dropped, then clenched. He understood. Richie wanted to win, at all costs.

After that, Red's life descended into a torrent of pain and agony. Richie made it all the way to the Semifinals, where he was knocked out by the future champion, and he didn't take too well to losing after what he had had to do to Red just to get there. He drove himself insane, trying to make his Pokemon powerful enough to win every competition he could.

Red was arrested, and his honor, his Trainer's License, and worst of all, his Pokemon, were taken from him. He was sentenced to never again carry Pokeballs with him-to never again be a Pokemon trainer.

Richie, in his insanity, figured that somehow Red would return to defeat him, so he hunted down and brutally slaughtered all of Red's captive Pokemon. Each of the creatures he loved so very much were murdered by Richie's powerful team. Pidgeotto, Charizard, Squirtle, Bulbasaur, Primeape, and so many others...all killed. Pikachu was the only one he thought could still be alive. He had managed to escape the Poke-prison he was sent to, or so the press had said. For all Red knew, he had died in the wild.

After that, Red was released, and he fled the Kanto region altogether. He had nothing left there to go back to. He stumbled upon Silver Cave by chance, and using his Pokemon dialect, he managed to convince the powerful Pokemon to let him live there in peace. He risked a lot gambling on his shaky hold on the language, but it payed off.

Red rubbed his eyes with his left hand. He had done nothing but forage for food and water since that day. He had had no contact with the outside world for four long, lonely, years. The only thought Red had left to cling to was the thought that someday, he would find Richie, and he would pay. He wanted revenge so badly he could almost taste it. Every night he dreamt of it. Every day he thought of it. And one day, he would have it.

Suddenly, a huge explosion rocked Silver Cave, and Red was pitched off this rocky seat. He flew across his large chamber, falling dangerously close to the edge of a long stone bridge. He got up quickly, sprinting out of his room to see what had happened.

All around him, Pokemon lay either dead or unconscious. Bodies of creatures that were so savagely strong that Red was terrified of them lay sprawled all over the interior of the cave. Red observed the room, and his eyes zeroed in on the blast center. He walked forward hesitantly, picking up a small rock for a meager self-defense, and leaned over the blast site. Red's eyes opened wide at what he saw laying before him.

"Pi…pikachu…pika pi…"