To the Reviewers and anyone reading this fic (I assume it is like over 100 based on the hit counter) Sorry about the wait. I got caught up doing other things but now I am doing this chapter . I don't feel the need for personal responses since there weren't really too many questions. However to Cdfe88 I wasn't even thinking about Austin Powers when I wrote that and the reference was lost on me until I remembered the Chinese girls . Also I wish you hadn't said that the ending to HP6 was sad. It kind of gave it away .

Enslaved Clones and Vengeful Aliens

Giovanni stood on one side of his personal battle arena deep beneath the ground of Veridian City. It was time to test his newest Pokemon and he intended to put it through its paces. Standing opposite Giovanni were his most loyal agents, Domino, Butch, Cassidy and Creig. Even though the mission to the Dragon's Holy Land had been a disaster the successful attack on Lavender Town and the unexpected, but most welcome, capture of Mewtwo had the leader of Team Rocket in a very good mood. Raising the GS ball Giovanni released his most prized Pokemon onto the field.

"Mewtwo." Said Giovanni "Come and serve your master."

In a flash of purple light Mewtwo appeared from his pokeball. His eyes had an eerie red glow to them and a black aura of power surrounded him. On his head there was a helmet like device which kept his psychic powers in check. He'd only been confined in the ball a short time, but already it was clear that he was on his way to Genocide Syndrome.

The Rocket Agents recoiled in fear from the awesome power emanating from the Genetic Pokemon. Giovanni smirked at their reaction. He waited patiently for them to get over their fear and when they didn't move he fixed them with an angry glare. Seeing the boss' irritation the four agents each raised a Master Ball and released a pokemon. Lugia, Articuno, Zapdos and Moltres came forth from their pokeballs and glared at Mewtwo. After being in the Master Balls for so long all emotions from the birds were gone save barely contained hate and rage.

"This will be a four-on-one battle." Said Giovanni "No time limit. I expect you to do everything in your power to defeat me." He paused to let his words sink in before shouting. "Begin!"

The Rockets didn't need to give their pokemon any orders. The intense training which Giovanni put them through gave them good battle instincts and they were able to fight much more effectively without being ordered. Still each pokemon had a receiver in their ear to get the commands from their trainers. Moltres was the first to attack. He flew as high as he could, which was about 50 feet thanks to the enclosed ceiling, and released a Fire Blast right at Mewtwo. The clone didn't even flinch and let the attack connect with him. Not wanting to be outdone Zapdos and Articuno used Thunder and Ice Beam respectively. Again Mewtwo allowed the attacks to hit him and they seem to have little effect. It was when Lugia prepared to fire an Aero Blast that Mewtwo finally acted. He released the pent up energy he'd been storing by using a Bide attack and slammed into the Diving Pokemon with all his might. The attack sent Lugia crashing into the wall where he made quite an impression on the 30-feet-thick titanium reinforced wall. Before the remaining birds could even attempt a counter Mewtwo had them all bound in a psychic grip and was slamming them into one another and the surrounding walls with gusto.

"Enough!" Said Giovanni. Mewtwo ignored him and continued to abuse the already battered birds. "I said enough!" Roared Giovanni again, this time holding up the GS ball and hitting a button hidden inside the cuff of his sleeve. The effect was immediate. Mewtwo stopped his assault on the pokemon and turned to face Giovanni waiting for new orders. "Return" Said Giovanni. Mewtwo returned to the GS Ball and the other agents returned their pokemon as well.

This battle had shown Giovanni several things. The first was something he already knew, Mewtwo was a very powerful pokemon, the second was that he needed to train his other pokemon more, then there was the fact that Mewtwo was already showing rebellion. It had taken too much effort to create the clone in the first place for it to escape once, but for it to happen again was out of the question. His first order of business was to test some stronger Slave Helmets to ensure absolute obedience from his newest weapon.

The boss started heading to his office when his cell phone started to ring. "Speak." He ordered.

"Boss this is field agent Mitch." Said the voice on the other line. "I'm sending you some info you should find very useful."

"And that would be?" Asked Giovanni skeptically. He decided not to comment on the euphemism of 'Field Agent' over the more common term of Grunt or his personal favorite cannon fodder.

"My team and I found out who has Suicune as well as another Lugia." Said Mitch "We also ran into some people who looked like Rocket Elites but…" He trailed off too embarrassed to mention Jessie and James.

"I see." Said Giovanni "I assume this information is now within the database?"

"Yes sir." Said Mitch

"Good, if it's worthwhile you may be getting a promotion." Said Giovanni.

"Thank you sir." Said Mitch. "I think I should mention that the guy who has the Lugia also has some rare pokemon that would be worth nabbing as well. He had a really strong Eevee that evolved into an Umbreon after the battle we witnessed. He also had a shiny Pikachu and a normal one. Both seem to have unusually high amounts of electrical energy."

It can't be… thought Giovanni "Did this person have black hair, brown eyes and annoyingly confident attitude?" He asked.

"Yes sir he did." Said Mitch

Ketchum "And you said a trainer was with him who has a Suicune?" He asked. Another grunt had said a Suicune was protecting a girl not too long ago but he had written it off as an overactive imagination combined with too much work.

"Yes" Answered Mitch "It was a girl about 17 with black hair and violet eyes. She seemed to be rather violent in battle and tended to have Water Pokemon. There are pictures of both of them and of the pokemon in the database now."

"Excellent." Said Giovanni "Keep an eye on them and keep me informed of their whereabouts.

"Yes sir." Said Mitch

Giovanni ended the call and continued heading to his office . He had several things to attend to and this new information was very interesting.

Brock sat in a corner in the mess hall contemplating his current situation. He was supposedly dead in the outside world and was now a member of an international crime rink. His family was being held somewhere and Mew only knew what kind of things where being done to them. He hoped that by his continual cooperation and acts of loyalty he was keeping them safe. He had no idea that Giovanni had already killed his parents for not cooperating and now had his younger siblings in the Rocket training corps. As far as he knew they were all 'safely' on the island prison where he was being held for the first part of his capture. Aside from his own personal problems was the guilt. He had done several things in the past few months that he thought he'd never do. Stealing, abduction, arson and murder. The heaviest death on his conscience was still Delia. He didn't know what he'd say to Ash if he ever saw him again. Since he didn't have much else to live for right now he decided to make the best of an otherwise bad situation. He trained his pokemon whenever he got the chance and still tried to give them the best nourishment he could. He had all his pokemon back with him, excluding Crobat, who had been mutilated beyond recognition at the hands of Domino, and he cared for them all deeply, even if he rarely showed it these days.

His musings were interrupted when someone sat down across from him. He looked up to see the purple eyes of Creig staring back at him.

"Hello Slate." Said Creig with false cheerfulness. There was no love loss between the two of them. Brock hated him for being the one who led the attack on the Gym and Creig hated Brock for constantly trying to show him up in front of the boss.

"What do you want?" Asked Brock venomously.

"Orders." Said Creig shortly.

"What do you want me to do now?" Asked Brock exasperatedly He was just tired of constantly having to do what this idiot said.

"Don't sound so sad." Said Creig teasingly "I actually have a present for you. The boss thinks you've shown great loyalty, even though we both know you'd bolt out of here given half the chance, and he wanted me to give you this." He pulled a Heavy Ball off his belt and handed it to Brock. "That's Aerodactyl's pokeball. The boss knows your fond of Rock-Types and I think he wanted to replace that useless bat of yours."

Brock silently took the pokeball and put it on his belt. "Crobat was not useless." Hissed Brock. "That bitch Domino is going to pay for what she did to my pokemon."

"You'd better not let the boss hear you talk like that." Said Creig mockingly "He might question your loyalties. I'd hate to see what happens to all those siblings of yours if you decided to get rebellious."

Brock simply glared at Creig for a few minutes before getting up and heading toward the door. He ran into Fiona on the way out "The boss is looking for you Slate." She said before going to join Creig.

Brock made his way toward Giovanni's office with a bit of dread. Surely the boss hadn't heard what he had said to Creig. Then again knowing the kind of person Giovanni was he wouldn't put it past him to have some kind of monitoring device in every crevice of the base. Steeling himself for whatever he was going to face in the boss' office he made his way to the double oak doors.

Deoxys raced over the Ocean at top speed. He had a mission and he intended to complete it. He was already on his way to reclaiming his body and Kyogre had the information he needed. The body of Groudon held immense power and once it was combined with his psychic abilities he was sure Kyogre would not be able to stand up to him, even with his type advantage. He could see Orre in the distance and by using Groudon's innate senses he could tell Kyogre was at the heart of it. Not to mention the storm clouds which loomed overhead.

"Soon everyone on this pathetic planet will know my wrath." Said Deoxys to himself "I will finish what I started millennia ago and this time there will be no meddling Dragon-God to stop me." With thoughts of unwrought destruction he made his way toward the heart of Orre where Kyogre was busy making a new part of the ocean.

Todd walked through the streets of Goldenrod heading toward the Johto capital building. It was a difficult task to get out of Kanto and an even harder one to avoid all the Rocket patrols around Johto, but somehow he'd managed to do it. Now he was on his way to see his uncle, Gavin Towers, who just happened to be a very high-ranking officer in the Johto Armed Forces. He wasn't sure what his uncle could do to help him, but he was sure that getting these pictures to him was the best thing to do. He'd promised Gary to get them to someone who could help and that's what he intended to do.

He entered the Capital Building and went up to the receptionist's desk. "Hello my name is Todd Snap and I'm looking for General Towers." Said Todd

"I'm sorry sir, General Towers is not seeing any visitors." Said the receptionist.

"He'll see me." Said Todd "Tell him who it is and I'm sure there'll be no problem."

"The general left specific orders not to disturb him." Said the receptionist.

"Can you just call him and tell him who it is?" Asked Todd exasperatedly.

"I'm sorry sir, but I could loose my job if I disturb him without his permission." Said the receptionist

"Look lady I'm his nephew and I have some very important things I need to discuss with him!" Yelled Todd

"Sir there is no need to scream." Said the woman in a monotone. "I am not aware the General Towers had any family and you are not on the list of approved entry, if you want to see him make an appointment."

"Fine when is the next available opening." Fumed Todd.

"Let's see." Said the receptionist while typing. "Here we are. The next opening I have for the general is one year from now at 3:00 p.m."

"WHAT?" Roared Todd "You've got to be kidding me!"

"Sir please keep your voice down." Chided the woman "The general is very busy and can't be disturbed."

"I've had it." Said Todd He walked toward the elevators only to be stopped by a very angry looking Machoke. Thinking the better of trying to use the elevators he made a mad dash for the stairs. Unfortunately his uncle's office was on the 12th floor. It took him the better part of fifteen minutes to reach his uncle's office but he did finally make it. As soon as he put his hand on the door handle he was grabbed from behind by the same Machoke who had fallowed him from downstairs. Thinking quickly he made one last effort.

"Uncle Gavin I need to talk to you!" He yelled

The office door opened and a man wearing a blue uniform with a few metals on a patch over his heart stepped out. He had short neatly trimmed blonde hair and looked to be in his middle thirties. He had piercing blue-grey eyes and a neatly trimmed mustache which matched his hair.

"Todd?" He asked.

The Machoke stopped dragging Todd away and waited for orders from the general.

"Yeah it's me uncle." Said Todd

"I haven't seen you in ages." Said Towers. "Let him go Stanly he's fine." The Machoke released Todd and headed back downstairs. Gavin ushered his nephew into his office and shut the door. "What brings you by?"

"Business actually." Said Todd. He reached into his bag and withdrew a small photo album. "I think you'll find these pictures highly informative."

Towers took the booklet from Todd and looked through it. He saw pictures of mutilated pokemon in what appeared to be a lab of some kind. In several of the pictures the crest of the Veridian Gym could be seen and in others people in black uniforms with Team Rocket's trademark 'R' emblazoned in the center. Most shocking of all were the pokemon battle pictures. They showed Giovanni commanding pokemon that had most definitely been enhanced by using illegal drugs. A couple pictures really caught his interest. One was of a Lugia facing down a Mew and another was a Ditto and several other pokemon facing down the same Lugia.

"Where did you get these?" He asked. In awe.

"Me and a friend of mine named Gary Oak got into the Veridian Gym and I took these while he battled Giovanni." Answered Todd.

"Oak?" Asked Towers. "Isn't he that nutcase who burned down Pallet?"

"No." Said Todd "He didn't do it. The attack on Pallet was in retaliation for him and I getting these pictures. It happened the same night we got these."

"It all makes sense now." Said Towers. "I've got to get these to the president. Stay here and I'll be back in a while."

He hurried out of the room with the photographs in hand and went straight for the president's office. He'd had his suspicions about Giovanni Rokai now he had hard evidence to back those suspicions.

Brock entered Giovanni's immaculately decorated office and stood in the doorway staring at the back of the huge swiveling armchair. He waited a few moments and finally Giovanni spoke.

"Slate, punctual as always." He said in an eerily friendly voice. "I have some footage I want you to look at Slate."

"Footage sir?" Asked Brock confused.

"Yes, sit down." Commanded the boss.

Brock sat down and Giovanni slowly turned to face him. He had an evil gleam in his eyes that didn't make Brock feel anymore comfortable. He hit a button and a screen came down. The screen flared to life and something that was clearly a pokemon battle was raging on the screen. On a closer look it was pokemon fighting a giant robot. The robot looked like a giant Kabutops.

"What is this sir?" Asked Brock

"Watch and you'll see." Said the boss.

What was unmistakably a Lugia was battling the robot and it didn't seem to be faring very well. There was a flash of red light and then a Suicune was in the battle. The camera went to a different shot and a girl with black hair and purple eyes was holding the pokeball that the Suicune had come out of. She looked awfully familiar to Brock but he couldn't place the face with a name. For some reason he was reminded of Misty. The angle changed again to an Eevee who looked to be trying to take on the robot by itself. There was a glow and then all of a sudden the Eevee released a lot of energy directly to the fleeing robot. What Brock saw next shocked him. Jessie, James and Meowth were flying through the air and one of them had Pikachu. They dropped him and the camera fallowed the electric-mouse's progress to the awaiting arms of his trainer.

"Ash!" Cried Brock before he could stop himself.

"So it is Mr. Ketchum." Said Giovanni "I just needed confirmation. I don't suppose you know who the young lady is with him?"

"No sir." Said Brock. Inwardly he had a suspicion of who that girl was. She had been holding a Psyduck that looked suspiciously familiar. He wasn't about to mention that to Giovanni though.

"I see." Said Giovanni "Thank you Brock. You are dismissed."

"Yes sir, and thank you for the Aerodactyl." Said Brock bowing slightly.

"One moment Brock." Said Giovanni. "Out of all the Gym Leaders I've managed to 'hire' you've shown the most loyalty and potential. I know that you were friendly with Ketchum and that you've done your fair-share of stopping Team Rocket's plans. I am curious as to why you have shown such little resistance."

Brock was barely managing to control his anger and keep a neutral mask on his face. This bastard had the gall to question why he was being cooperative. What did he think the reason was. His family was being held hostage and up until recently at least one of his pokemon. Not to mention his own life was on the line. Thinking quickly he came up with something to express those thoughts in as polite a manner as possible.

"I was under the impression that you would accept nothing less than total obedience from your…'employees'." Said Brock "I was told that if I did not cooperate my family and pokemon would suffer. I also realized that it would be much easier to cooperate and make the best of this situation."

"That is unfortunate Brock." Said Giovanni "I regret to inform you that your parents resisted when we went to recruit some of your brothers and sisters. One of the team members may have accidentally ordered his Rhydon to use Hyper Beam on them. I hope that this doesn't damage our relationship.

This was the last straw. He had submitted to them for too long. Gary's words from the attack on the Dragon's Holly Land rang through his head. "…Gramps and May wouldn't want me to sell out to the likes of you," Brock knew his parents wouldn't have wanted him to do any of the things he'd done. It was too bad it took them to die to realize that. Right now he had to think of a plan to get out. He couldn't get his siblings out now and they'd probably live since they were in the recruit program. For now he decided to keep up appearances until he got into a more private area were he could think. "I understand sir." Said Brock "You warned them the same as me, they suffered the consequence." It felt sickening saying it, but he knew he had to keep up the act.

"I am glad we are on the same page." Said Giovanni "I am sorry for this inconvenience but I hope you remember that loyalty is rewarded and betrayal is punished."

Brock nodded and left the office. He wasn't sure what he was going to do but he knew he was doing it soon. He past a set of heavily armored doors and he knew what was behind them. If he could bust Sabrina and her pokemon out he could escape much easier. He contemplated getting professor Oak out too. He knew Gary would never forgive himself if his grandpa or sister were hurt and Brock knew where the both were. He just hoped he wasn't calling Giovanni's bluff by attempting to escape.

Orre stretched out in all directions from the tip of Mt. Battle. The stadium below was deserted for once since the torrent of water coming down made it impossible to hold pokemon battles. And the constant mudslides were of no help either. Kyogre was pleased with his handy work. He was sure this would get Groudon's attention and this time He would finish the fight before that fool Rayquaza could use his powers to make them stop. And once Groudon was out of the way the world could be submerged in water and then…

Kyogre really wasn't sure what he would do after that. He hadn't really thought about it too much. So deluded was he by his own ambitions that he couldn't focus much on anything. Unlike Groudon, who had managed to open his eyes slightly thanks to Mewtwo, he couldn't sense the eminent danger that was heading straight for him. He had no idea that his former master was only a mile away and would be right next to him any second. He also had no idea that a Solar Beam was fully charged and steadily being made even more powerful thanks to Deoxys' psychic energies and Groudon's natural ability to have sunlight no mater how many clouds were in the sky.

This was unfortunate for the Sea Basin pokemon because Deoxys was now right behind him and he did not hesitate to release the devastating blast of concentrated sunlight right into the center of Kyogre's back. The water titan screamed in pain in rage as the attack seared away at the flesh between it's two fins. It crashed into the muddy slope below making the ground shake and sending an enormous spray of mud all over the place. Deoxys lowered himself in front of it's former servant and stared down at him with the eyes of it's ancient enemy.

"Where are the components to my body." He asked simply.

("Y-your dead.") Said Kyogre hysterically. He knew exactly who he was talking to and did not want to be talking to them.

"I assure you that that is only half true." Said Deoxys. "My body has been…disassembled, but my spirit is whole. Your friend Groudon found that out the hard way." He paused letting his words sink in. "Now I will ask you again. Where are the three components?'

("I don't know.") Said Kyogre. ("I swear I don't know.")

"That is unfortunate." Said Deoxys "Because now that I don't know where my old body parts are I have to make new ones." With a wave of his hand Kyogre floated into the air. The hole in it's back started to grow and bone and tendons could be heard cracking and ripping while Kyogre screamed in agony at the torture put on it's body. After several minutes of this process the only way the body could be recognized as once being Kyogre was because of the blue color. However Deoxys wasn't done crafting his new body yet. He gave Groudon just enough control to feel his body begin to change. Much in the same fashion as Kyogre's body a hole appeared at the base of Groudon's neck and his body slowly and painfully began to turn into a red and gray mass. The two masses of flesh bloated in the air and suddenly rammed into each other and began to merge together. White light began to radiate from the floating mass and it slowly turned into a humanoid form. It was very tall and had long legs and even longer arms. It was mostly red but had a blue face, hands and feet. Blue spikes also came out of its back and arms. The head was sunken in slightly so that it almost looked like it was wearing some kind of armor. Deoxys was reborn and he had only two things in mind. Kill Rayquaza and devastate the earth and not necessarily in that order.

A/N: I would like to say I am sorry for the long wait for an update. I just got sidetracked with other things and it was hard to get back into writing this. I will do my best not to let that happen again and I will try to update again sometime over the Thanksgiving holiday. No promises but I may even update twice . Please review and let me know what you think of this chapter. Please be constructive as flames will be laughed at. Again I am sorry for the wait.