Tsunekazu Ishihara, Satoshi Tajiri, Nintendo, Game Freak, Creatures Inc., 4Kids Entertainment, and KidsWB own Pokémon.
Rating – PG-13 for mild violence and language.
Author's Note – This is a re-write of a fiction I typed up almost three years ago, but now it has been re-written to be in a trilogy, and to not be as poorly written as the original was.

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Brainwashed
Part 1
Psy Blade

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A fourteen year old boy crept through the depths of the Team Rocket Head Quarters, searching for any information on members of Team Rocket he could interrogate information out of that he could use as evidence that Giovanni was the leader of the high ranking criminal organization. He had to be extra careful because he was well known to these crooks, he had taken down many a member and sent them to prison, and he was most wanted number one of this team. As he crept through the shadows, he noticed voices coming from a door that was slightly cracked open.

"Have you taken care of your grandson, Samuel Oak?" said a gruff voice, which the boy identified as Giovanni.

'Oh, no, don't tell me they killed Gary!' thought the boy, putting two and two together.

"Yes, he has been sent off on another journey for me, now what is the next step of our plan?" asked a man on the videophone whose voice could only be Professor Oak's.

'Phew, they didn't kill him after all. That's good, but what's this plan they're talking about?'

"We have sent agents to capture the boy with that pikachu, then he will be transported to your lab in Goldenrod for the 'experiment'," replied Giovanni.

'Oh, shit! That's me! I hope they don't… know… I'm… here…! Oh no, the Professor is the one who sent me here! I've got to get away!' though Ash as he turned around to run away, but coming face to face with a huge Rocket guard.

Ash then wished he had taken his Pokémon along, but Samuel had said that he had to stay covert.

"In fact, he should be here by now. You can bring the boy in now, Surge," mocked Giovanni, turning around to face the door.

The man that Ash had just realized was the old Vermillion Gym Leader shoved him into a cold, dark and creepy room. Looking around, Ash noticed three other trainers shackled to the wall to his right, all with fearful expressions on their faces.

"Lock him up with the rest of them until the transport arrives," ordered the boss.

Surge shoved him over to another set of shackles on the wall, and locked the huge metal cuffs around his arms and feet.

"Watch them," said the boss, glaring at Surge as he walked out.

"Oh, sure, I'll watch them," he said with a grin.

The big man then walked over to Ash and proceeded to punch his chest, crushing a few ribs, while knocking the wind out of Ash, "That was for ruining my reputation, baby!"

Ash coughed up blood, and noticed the other trainers staring at him, "What? Never seen someone get punched before?" he asked with a hint of annoyance in his voice, which made them turn away.

Surge, looking proud of what he did, walked over to the door, and walked out. He was visible through the glass, obviously guarding the door, although it didn't matter much, there was no way out of the shackles.

'If only I could reach my belt,' Ash thought, remembering the lock pick he had used to get into the base in the first place.

The other trainers started talking amongst themselves, and then one of them asked Ash, "Who are you?"

"Ash Ketchum, from Pallet Town," he replied, coughing a little.

"No way, you're the Ash Ketchum, the kid who came sixteenth in the Indigo League, beat the Orange Crew, placed fifth in the Johto League, and came in third place the second time at the Indigo League?" asked the same one.

"I'm that famous, huh?" he coughed, "Never thought just doing that would make me famous."

"So why did Team Rocket capture you?" the last one asked.

"Because I'm on a mission for Prof. Oak, supposedly. I was going to be gone a few months. And it so turns out that he works for Team Rocket, which his reasoning for it is beyond me."

"So that's what they were talking about," he replied.

Ash was getting irritated that they were asking so many questions, and couldn't really decide if he was thankful or not when Giovanni came back in to take them all to Goldenrod. Surge, and a few other Rocket Grunts with guns followed him into the room, and then Giovanni noticed the blood seeping from Ash's mouth, which just made him smirk.

The ex-lieutenant was assigned to unshackling them, and herding them out to the back of the HQ.

They were all careful not to run away because the grunts had guns on them, plus the Gym Leader amongst them was big enough to take on twenty trainers their size.

When they all walked up the ramp into the back, they noticed four cells, one for each of them, one cot hanging from the wall in each, and three meals placed on plastic plates on the floor.

They were all shoved into a different cell, and the doors were locked.

Once the Rockets and their boss were out and in front, the trainers began to talk.

They talked about why they were there, what they had done to get on Team Rocket's wanted list, and tried to bring Ash into the conversation more than a few times, he just ignored them and silently ate one of his meals, then decided to rest, to heal from what Surge had done, so he climbed up onto the cot, covered himself, and fell asleep.

---

As the sun slowly rose over the horizon to the east, an alarm clock went off in a one Misty Cerulean's bedroom. Silently, she reached over and pressed the sleep button, turning it off for ten minutes, and falling back to sleep. Slowly, her subconscious reminded her conscious of how important today was, she was to become an Elite Four member today, after Bruno, one of the original Elite, had finally resigned, saying it was time to give someone else the chance to be an Elite. Misty shot up in bed, and looked at the alarm clock, they would be there in an hour. Cursing at having to get up so early, she rose out of bed and went into the shower.

About twenty minutes later, she walked out of the shower, drying herself with her towels, and quickly got dressed in her usual attire, a black tank top, navy blue jeans, and white slip-on shoes. She then continued her early morning routine of brushing her teeth, combing her hair, putting it in a sideways ponytail, and cooking breakfast.

As soon as she was done, the doorbell rang. Wiping off her mouth with her napkin, she got up and walked to the front door of the Cerulean City Gym. When she opened the door, none other than Lance himself greeted her. He was the current Indigo League Champion, even though he was one of the original Elite, and had authority on who became one.

"Hi, Lance," she greeted him.

"Good morning, Misty. I hope I didn't have you wake up too early. As you probably already know, Bruno has finally resigned, and we want you for the next Elite," he replied.

"That's what confuses me, Lance, why me? Why not Gary Oak, Brock Quartz, or Ash Ketchum? They're all better than me," she told him.

"Well, Ash and Gary have shown greater potential than you, no offense, but they do not want to be held back by this job instead of becoming a Master, and Brock, well, he said he had too much responsibility being the caretaker of his siblings," he explained.

Remembering how rude she was to not invite Lance in, Misty asked, "Would you like to come in and talk about this further?"

Lance nodded, and they walked to the living room, each sitting at a chair, continuing their conversation.

---

Brock finally got some time to rest after taking care of his siblings, who at their age, should be taking care of themselves. He had heard about Bruno resigning, and then Lance asking him to be the next Elite, but refusing, and he wondered who accepted Lance's offer. There were only a few gym leaders who were excellent enough trainers to be an Elite, and he would have to wait until the announcement of who was next aired on Thursday.

Figuring out a way to find out early, he went to the phone to call around, starting with Misty. He dialed the number for the Cerulean gym, hoping someone would pick up.

After three rings, a very tired, and disgruntled, Lily picked up, "Hello?"

"Hi, this is Brock Granite, I was wondering, is Misty around?"

"Why, are you her boyfriend?" she replied, still to tired too register anything.

"No, that would be Ash, I'm one of her other friends, and the old Pewter Gym Leader. I'm calling to know if she knew who would become the next Elite."

"Oh, well she's talking with Lance right now, call back later," she said with a yawn.

"Okay, thank you!" he said hanging up.

"Well, that was a weird way of finding the answer to my question."

---

Even in his dreams, Ash could feel the truck stopping, and the gears shifting to park. Although he was still tired, and his ribs still hurt, he decided to get up, otherwise the Rockets would wake him up, and he had a feeling he didn't want that.

Sitting up, and rubbing his eyes, he looked around to see the same thing he saw the day before, except for the fact that the three trainers were now asleep.

"Hey, wake up! We've stopped," he yelled at them. Although they were annoying, he didn't want them to be woken up by the Rockets, which would probably involve some sort of violence.

They each rose from their cots sleepily, one after the other, and looked around.

"Why'd you wake us up?" one of the ones Ash hadn't seen earlier asked.

This one he instantly recognized as Duplica, which surprised him, "We've stopped. And I doubt any of you would want to be woken up by any of our escorts," he explained.

They all nodded in agreement, and got out of their cots.

The doors leading out unlatched and were opened, and Surge stepped in.

"Alright, babies, time to go," he said, unlocking the cells.

They walked out, and were herded into an underground building. Before Ash was shoved inside, he quickly looked around to see if he could find out where they were, and had no clue, he had never been to this part of Goldenrod.

Once they were inside, they were separated and sent to four different rooms. As soon as Ash walked into the room he was sent to, he noticed it was a shower obviously they weren't completely heartless. He also noticed some clothes near the door, a black t-shirt, black shorts, and a box that was labeled, "Place shoes here."

Ten minutes passed, and Ash walked out in his new attire, wondering what they were planning. The others came out a few minutes later, dressed in similar clothing.

Without a word, they were forced to proceed through another door, where they saw four metallic cylindrical devices, all with triangular windows. Samuel then pressed a button on a control panel connected to each device, and half of the cylinders opened up, revealing a nasty looking needle, and some other peripherals.

"Place them in each of these," he explained.

Ash saw them each get pushed into one, and when he was shoved into it, he heard two of them trying to resist, but then there were a few shouts of pain, and they stopped. Since he did not want to have the same fate as them, he just quietly did as he was ordered.

Once he was standing against the padding at the back, one of the scientists he hadn't seen before placed pads connected to wires on his head. He then put restraints around him, and before he put a mask over his face, he said, "Nice knowing you, kid!"

Ash panicked at that and was about to try to escape, but the mask was placed over his mouth, and the sweet smell of chloroform greeted him, putting him into a deep sleep.

---

{They have the boy…} the psychic voice of Mewtwo rang throughout their minds.

His two closest friends, a pikachu and meowth, wondered what he was talking about.

{Giovanni has Ash,} Mewtwo explained.

*So what? He does not concern us!* exclaimed the pikachu who still did not think humans were all they were cracked up to be.

{You are too quick to judge them, not all humans are bad, as he has shown us on more than one occasion,} stated Mewtwo, picking up on the pikachu's thoughts, {And yes, he does concern us. He knows our location. If Team Rocket delves too far into the past few years of his mind, they will know about us, and they will find us.}

*I knew we couldn't trust him! Now we'll have to find a new home!* cried the electric rodent.

{This was not a matter of trust, it would not be his fault, and we did not know that that disgraceful company would put him through this.}

*Can we help him in any way?* asked the ever wise meowth.

{No, there is no way we can help, this has to play out by itself. If we were to interfere, then we will be discovered.}

*I feel sad for him, for all the things he will do in the next few months, maybe years,* explained the meowth, solemnly.

*Well I don't! He can rot in hell for all I care!* the mouse suddenly screamed.

This seemed to tick off Mewtwo, who raised his mind's voice, {Do not judge humans so poorly, or you may find yourself to be dead because you refused the help of a human! If I had not accepted his help, then I, too, would be dead. You need to get off your high horse and learn more about the human race!}

The rat cowered in fear, and the meowth sighed, her friend might not ever learn, until it was too late, which was something she did not want to think about.

---

"Come on, babe, why won't you go out with me, I'm a better trainer than that Chosen One loser, so why don't you forget him and come with me?" asked a largely built man with brown hair and green eyes.

Melody grew agitated and replied, "How dare you insult the one person who saved this whole planet!"

"So he saw a few legendary birds, so what? So he stopped them from fighting, so what? Anybody could catch those birds," he replied superiorly.

"That's highly doubtful because if any of them are ever captured, the world will be in turmoil and then all plants and animals will cease to exist. Not even the Chosen One could catch any of the Titans, the three most powerful legendary birds of their species. Sure, anybody could catch the lower articunos, zapdos, and moltres, but no one could capture a Titan. Besides, mere Pokéballs can't hold them…" said a voice from above them.

The voice came from a teenage boy with brown, spiky hair. His eyes weren't visible due to the glare from the sun. He hopped down from the ten-foot incline, put a hat on to hide his eyes once again, and grabbed a Pokéball. "Want to see if you really are better than the Chosen One?" the boy grinned.

"You're not the Chosen One, he has black hair! You look like a scrawny trainer, I doubt you could stand up to me!"

"I may not be Ash, but I'm the next best trainer!" he replied, throwing out a Pokéball, which split and the form of an Umbreon materialized.

"Hah! An umbreon, easy match for Hitmonlee!" he grinned, sending out the kicking fiend monster.

The umbreon and the boy grinned, seeing how easy of a battle this would be, the hitmonlee was exhausted, his deep breaths a sign of this, and he had many untreated wounds. "Finish it off with a Quick Attack!"

"Use Agility, Hitmonlee!" ordered the bozo who kept his Pokémon in such a bad status.

The hitmonlee was too tired to dodge, and ended up getting knocked down.

The idiot trainer recalled him, then sent out a butterfree, who also looked in bad condition.

Before its trainer even called out a command, it fell down, near death. The boy gasped, and ran over to the fallen bug, taking out a first-aid kit.

The trainer looked angry that his monster fell down without even fighting, and walked over to it, and was about to hit it, when he was elbowed in the gut by the boy. As the trainer lay on the ground, the boy took the Pokéballs off his belt, and took his Pokédex.

"Those are mine, you thief! Give them back! No one can take other people's Pokémon!" he gasped, still buckling over.

"Yes he can," Melody spoke up, "When a trainer abuses their Pokémon, another trainer has the right and obligation to take that trainer's monsters and get them to the nearest Pokémon Center. Besides, this here is Gary Oak, son of Professor Samuel Oak, and also a part-time scout for the Elite Four."

"What?" yelled the trainer, "How was I supposed to beat him? He's probably way better than that Chosen One piece of shit!"

"Don't talk about my friends that way, you loser, and besides, he beat me in a fair battle two days ago."

---

"So I get over two thousand dollars a month? Wow! That's a big offer!" exclaimed Misty.

"Well, Pokémon battles are backed by the government. Of course, there's a catch, you need to be ready to get to Indigo Plateau on a moments notice, you'll have to accept all challengers, and you'll start as the first of the Elite Four, but as you prove yourself to us, you will be put back to one of the other three positions," Lance explained.

"How am I going to get to Indigo so quickly? There aren't any Long Distance Warp Tile stores anywhere around here, and I don't exactly have a car," Misty stated.

"You'll get your own house up on Mt. Silver, which has a Warp Tile for the Elite at the Town Center," he replied.

"My own house? Wow…" she said, getting starry eyed.

---

"So you're Melody, huh? Never thought I'd meet one of Ash's old friends," Gary said, looking out towards the three islands that now have a place in history.

"Thank you for dealing with that trainer earlier, he was really getting on my nerves," she replied, sitting down next to him on the bench.

"Think of it as a public service. Besides, Ash is my friend, too, and I can't stand people disrespecting anybody, or anything," his gaze shifted to the shrine below them.

"It was still nice of you to get rid of him. So, what brings you to these parts?" Melody asked sweetly.

"I'm on a capturing mission for my grandpa. I was sent here to capture the unusually strong Pokémon on the three islands, and I just happened to be passing through here on my way. Why were you hanging around him, anyway?"

"I have to as the ritual performer. It's my job to hang around the trainer, and then do my ritual of the Song of Lugia at the party before they set out to get the orbs the next day." She explained.

Seeing a crime take place, he stood up, saying, "Speaking of the orbs, they're being taken from the shrine."

They both dashed down to the shrine, and stopped the person from getting away by blocking his path. This man looked very similar to the trainer from earlier that day, but this one wore a red Team Rocket uniform with a black R, the sign of a covert operations squad member.

"So you're part of Team Rocket, no wonder your Pokémon were so poorly trained!" growled Gary.

"Huh?" came the reply, "Oh, you must mean my brother. Yea, he can't train them too well. Anyway, I'm out of here!"

He dashed to get away, but Gary tried to punch him. The Rocket dodged, but dropped the orbs. All three gasped as they fell, as if in slow motion, before making contact and shattering. After the orbs shattered, three gems, each the color of their respective spheres.

Suddenly there were three screeches and a low growl, making the three people aware of a few Pokémon flying above the shrine.

{You shall not have the Destiny Gems, they belong to the Chosen One! We will not let you have them!} screamed the mind of Lugia.

The Rocket looked thoughtful for a moment, then picked up the gems, turning to make a hasty retreat.

"There's nowhere to run!" Gary smirked as the man came to the edge of the cliff the shrine was on.

The Rocket turned around, with a huge grin on his face, saying, "Who said I had to run?"

This made even Lugia confused, and then the Rocket held up a detonator, pressed the button and said, "Sayonara, the bomb is set for fifteen seconds, it'll blow this shrine sky high!"

Gary looked scared as the agent pressed a button on his watch, and disappeared, as if he teleported.

Immediately after, explosions rocked the ground, and then the cliff began to split apart, falling into the water, taking Gary and Melody with it.

---

"How exactly does this work, Professor?" Giovanni asked Oak.

"Well, most people think that brainwashing is completely wiping their memory, that is possible with a disease or serum, but not with a machine, and not the way we want. With this machine, we can wash, or erase, the memories we feel they don't need, while keeping the ones they do need. To do this, we have an electro-magnetic pulse amplifier amplifying the brain activity in the memory zone. This amplifier is set up to an electro-magnetic pulse translator, which translates these pulses into visuals. The amplifier is used to sharpen the image, and create a more accurate view of the memories," he explained.

As soon as he finished explaining it, the scientists started the machines up, illuminating the insides, showing the peaceful look of the trainers in each capsule. Immediately after, needles struck through their skulls into their brains, pinpointing the memory zone. Visuals popped up on the monitors, displaying their memories. With all the memories they all have, this would be an excruciatingly long process, lasting days, maybe weeks.

---

To be continued…