HP PKMN MSTR 3

It was finally the day that Harry would challenge his father to a Pokemon battle and Harry was looking forward to it. It would likely be his greatest challenge yet, but Harry wasn't sure why he felt that way and or why he had brought his Charizard with him. It was his strongest Pokemon, but Harry didn't truly understand the need that he felt. Still, Harry had him as a last resort.
Harry entered the Viridian City Gym. "Father! I challenge you!" He called out.
"I've been expecting you, son," Giovanni said, sitting on a raised platform in the shadows. "I've been keeping an eye on your progress and you have made me extremely proud. You have risen above any expectations that I had for you and have become very powerful and skilled. My perfect heir.... When you lose this battle, then you will take your rightful place and get involved in Team Rocket's activities."
"I have no intention of losing. And I won't waste my potential dealing with the idiots that you employ. When this day is over, you will know that you never stood a chance of victory or forcing me to become a common thug." Harry said coldly, truly angry that his father would try forcing him to become something he despised and that he would try bullying him into becoming a criminal.
"Very well," Giovanni said with a visible frown, but still pleased that Harry didn't outright refuse. Harry was too skilled to lose as an heir and him being arrogant enough to dismiss him as threat would be a great boon, Giovanni thought, pleased with the out come. "This will be a six-on-six battle, with substitutions allowed, and when you lose, you will take your rightful place as my heir. Go Golem!"
"Go Kingdra!"
Giovanni started the battle off by having Golem use Rock Slide, which was countered by Water Pulse and followed up with Hydro Pump; blasting Golem into a wall, unconscious. Giovanni returned Golem and sent out Nidoqueen, which Harry knew could use Thunder.
"Thunder!" Giovanni said, going right for the kill.
"Dodge and use Ice Beam!" Giovanni had Nidoqueen dodge it, but she was forced on the defensive and was eventually hit by an Ice Beam and rendered unable to battle, and angered Giovanni, who needed to defeat Harry's Kingdra and weaken him before unleashing his big surprise.
"Go Nidoking, use Thrash!"
Harry had Kingdra dodge and use Water Pulse, which was dodged, but now Harry's Pokemon was forced on the defensive, but, unlike Giovanni's Pokemon was in a fighting retreat and weakening Nidoking badly.
"Thunder!" Giovanni ordered desperately, needing Kingdra beaten.... This time, Kingdra was hit and unable to battle.
"Go Blastoise!" Harry said. "Use Hydro Pump!" Nidoking was unable to dodge, so Harry had it followed up by another, which rendered it unable to battle.
Giovanni returned Nidoking and sent out his Dugtrio and had it use Dig. Harry replied by having Blastoise soak the ground in water to make it move easier and give hints as to where Dugtrio was.... After figuring out where Dugtrio was going to attack, Harry had Blastoise use Protect, and once Dugtrio surfaced use Hydro Cannon. Dugtrio was easily defeated and Giovanni returned it and sent out his Rhydon, which was quickly defeated by yet another Hydro Cannon....
For some reason Giovanni was smirking at his son. "Ready to see my final Pokemon?"
"No. I'm just standing here to hear you speak," Harry replied sarcastically, angering his father with his disrespectful attitude. Harry quite frankly didn't care. His father wanted to mold him into someone that he just wasn't interested in being, and Harry was questioning whether or not his father truly loved him for who he was.
A metal door was opened and Harry sensed a great deal of psychic power and his Blastoise was blasted into a wall, but remained conscious.
"What is that?!" Harry asked in shock.
"A clone of the Legendary Pokemon, Mew. Now, surrender and take your rightful place as my heir. Your Pokemon don't have to get hurt anymore." Giovanni said arrogantly, already expecting his son to surrender.
What Giovanni wasn't expecting was laughter.
"You think having a Legendary Pokemon guarantees you victory?! There are many powers in this world, old man, and I've made it my mission to master them!" Harry said, rubbing his Mega Ring with glee. "Blastoise! Mega Evolve!" Harry said, confusing Giovanni. Confusion turned into shock as power emitted from Harry's Mega Ring and Blastoise and light enveloped Blastoise as she evolved into her Mega-Evolved form.
"Now! Dark Pulse!" Harry ordered and Harry watched as the devastating attack was launch into the air and rained down upon Mewtwo's Barrier, creating a crator from the force of the attack and heavily damaging the Gym in the process. "Dragon Pulse!" Harry ordered, and Mewtwo was blasted into a wall, damaging his armor. Blastoise spent the next five minutes brutally blasting Mewtwo into submission with Pulse attacks. Mewtwo was eventually overcome and defeated.
"You shouldn't have tried forcing me to become criminal...." Harry said, approaching the defeated Mewtwo. "Most would be pleased to have child who is a model citizen, but I guess you're just an exception." Harry caught Mewtwo in a reverse-engineered Master Ball and telekinetically pulled the Earth Badge to him. "You should retire and disband Team Rocket. I was willing to hope that you could change, but you attempting to force me to become a monster finally destroyed that hope. Well done."
"Harry...." Giovanni said angrily, having just lost his best Pokemon and perhaps even his only son.
"You can make sure that I'm given my rightful prize of 8000 Pokedollars and ensure that no one disputes my having the Earth Badge. We both know that I more than earned it." Harry recalled Blastoise and teleported away.
-----------------------------------------------------------------------------------------------
Harry had over three months to train for the Pokemon League and several new Pokemon to bond with, but Mewtwo just wasn't cooperating. Harry told him that his father was just using him as a weapon and didn't truly care for him, and Mewtwo accepted that, but distrusted Harry for catching him. Harry was at a loss as to what to do with Mewtwo, it distrusted humans in general and Harry hadn't gained much goodwill with him, even after restoring his memories. Mewtwo didn't want to fight for humans and Harry wanted to take the hard path and not use legendary Pokemon in battles, and he absolutely refused to have his skills be doubted because he used legendary Pokemon instead of Pokemon that required actual skill. In the end, it was Mew that solved the problem and took Mewtwo under his wing, and Harry even regained a Master Ball by freeing Mewtwo.
Harry found himself an island that was unclaimed and had no legal owner and placed it under the Fidelius Charm and would be warding in his spare time. He couldn't do a lot in the way of wards, but the older wards predating Wandlore were easily doable and Harry was glad that he knew them. It was already quite large, but Harry also magically expanded areas and made Pokemon habitats, training areas, Pokemon battle-fields, and a refuge for abused Pokemon. The Castle was Harry's favorite feature though....
It was four stories tall and each bedroom had its own bathroom and walk-in closet, but the Master Bedroom was fit for a king. It had a Great Hall, cellar, twenty bedrooms, and, of course, a kitchen. It was the throne that was what tied it all together. It allowed Harry to monitor the entire island and all of its inhabitants. The castle was shaped with transfiguration and the power of his Pokemon, who melted rock and Harry shaped it and enchanted it. It would take time for Harry to stock it with technology and adapt the technology to magic, but it would at least have electricity before the Indigo Conference began.
Protected by magically reinforced walls and watch towers, Harry intended for this castle to stand for over a thousand years.
Harry finally evolved his Rhydon into Rhyperior and it learned the Rock Wrecker move.
Harry had his Pokemon at what he believed to be the Champion-level, meaning Harry felt they had the raw power to match the likes of Lance.
Harry wasn't training right now though, he was meditating. Death had communicated its desire to speak with him in his mind and Harry was making that easier.
"Hello, Master," Death greeted. "It seems that Fate has placed you where you can fight on the side of good once more.... She wants you to defeat Team Rocket and several other villainous groups who abuse Pokemon. She placed you as Giovanni's son so that you could defeat Team Rocket more easily and free the Kanto Region from their grasp. You were fortunate enough to meet and impress Lance, who is affiliated with the G-Men and Pokemon League. Your natural talent and some mild interference from Fate has given you all the skills and resources that you need to defeat Team Rocket."
"How will I defeat Team Rocket? After the Indigo League I'll need to train and begin the Johto League."
"You could still train briefly before beginning the Johto League, and with your knowledge of Team Rocket you can end them quick.... Also, Giovanni is leading a force to question you about Mewtwo's whereabouts and you can invade his mind again for updated information. If you need extra power then you need only create a familiar bond with your strongest Pokemon, perhaps the ones that can Mega Evolve. It would allow them to grow moderately stronger in the short term and much stronger in the long term." Death said.
"He knows where my Island is located?!" Harry questioned in shock.
"No," Death said, easing Harry's mind. "But once you're off it, he will track you down. Also, your island is formerly volcanic and has a decent deposit of gems, coal, gold, platinum, and silver; Fate and I created it with our powers. I would suggest that you establish a familiar bond with your starters and then go wait for him, but remember that your magic is finite and less familiars will equal more powerful Pokemon."
Harry began thinking about his best options. Charizard, Dragonite, and eventually Tyranitar would give him two augmented Pseudo-Legendary Pokemon and an uber powerful starter that can also Mega-Evolve. But was it cheating? Harry didn't use Legendary Pokemon for battles and he had to wonder if it was doing the same thing by making Pokemon familiars. Harry was torn, but also knew that eventually a trainer would use Legendary Pokemon against him.
"You're right, they will," Death said, having listened to Harry's inner monologue. "If you make them your familiars, it wouldn't be cheating; at least not any more than using Legendary Pokemon would be. The power they would wield would be a result of the trainers power, you, and their power uniting and that's what Pokemon battles are all about. There are similar powers like Bond Phenomenon or Primal Reversion, but this lacks the side-effects and wouldn't be anywhere near what that power would achieve. Not for a while anyway."
"I'll do it and I'll defeat Team Rocket." Harry said.
"Wonderful! Good luck saving the world!" Death said, before vanishing.
Harry sighed, and began forming familiar bonds with Charizard and Dragonite, while wishing he had the power to do it with all of his Pokemon. Sadly, he would never be that powerful. Oh Harry knew that he was powerful, far more than Dumbledore, Grindelwald, Voldemort, and even Merlin combined, but familiar bonds took quite a bit of power to achieve and form. At his current power, he could only form ten such bonds and that would waste his power. Harry would still train his magic when he could, though, and would seek to grow his power much further and be able to bond with more Pokemon.
His Charizard and Dragonite were now his first two familiars in this world, and Harry was as ready for war as he would ever be, so he teleported away.
-----------------------------------------------------------------------------------------------
Harry opted to wait near Team Rocket HQ for his father to find him. At least that way he wouldn't have to travel far to carry out his first act of war; if he decided to strike now. Harry wanted to end this before the Indigo Conference began, and after reviewing what he knew of Team Rocket he decided it was possible. Frequent teleportation and his powerful Pokemon would enable him to achieve a speed and stable victory.
Sure enough, Giovanni arrived near him; via helicopter.
"I'm guessing that you decided against retiring and disbanding Team Rocket," Harry said, in lieu of a proper greeting.
"It was never even under consideration. I will rule the world! Now... where is Mewtwo?" Giovanni said angrily.
"Your actions caused him to hate humanity and he couldn't be trusted, so I dealt with him." Harry said, though Giovanni figured that Harry locked Mewtwo away instead of killing him like he implied.
"Return Mewtwo to me, Harry, and I'll let you keep all of your Pokemon but your Blastoise." Giovanni said, surprisingly arrogant about his chances of victory. Harry thought he had beaten that arrogance out of him.
Harry smirked. "I figured that you wouldn't leave me alone and would keep harassing me until you got what you wanted, so I have a counter-offer. Every member of Team Rocket will release their Pokemon and will surrender and allow themselves to be taken prisoner. If they refuse, I'll destroy two Team Rocket bases a year until all are dead or in prison. I refuse to let your evil continue any further." Harry said, to Giovanni's anger. It was a lie, of course; Harry would end them in a matter of two weeks.
"You're outnumbered and I can send entire armies of Pokemon against you."
"And I can send individual Pokemon against you with the power to destroy your armies." Harry replied. "And Mega-Evolved Pokemon are useless without the trainer they're bonded with, so Blastoise would be utterly useless to you."
Giovanni rolled his eyes, believing Harry was lying. "Seize him!" Giovanni ordered, and two Grunts stepped forward, attempting to look menacing. Harry smirked and blasted every member of Team Rocket back and pulled their Poke Balls to him. That was also Steelix's signal to damage the entrances of Team Rocket's HQ. Harry pulled his father to him and then began searching through his mind, getting a lot of useful info....
Names of clients and agents, bases, projects, bank accounts, and locations of plenty of evidence for conviction. Harry Obliviated his father of the psychic intrusion and then cast a sleep spell on the nearby Team Rocket people and bound them in chains that he had stored in his magically expanded bag.
Harry sent out his Dragonite and Charizard and began sieging the base....
The fence was quickly destroyed by Steelix who rose from the ground and blasted the front entrance with Hyper Beam. Harry, however, Apparated inside and began copying all the data to a portable hard drive while stunning and binding the Team Rocket goons. Once done, Harry portkeyed his prisoners away and went to retrieve all the stolen, caught, or poached Pokemon.
When all was said and done, Harry had taken hundreds of prisoners and had Pokemon that would either be returned to the wild or their rightful trainers. Harry had made sure to remove peoples memories of his magic. Apparently though, he had drawn a lot of attention... from the International Police and Pokemon G-Men.
"Harry, right?" Lance asked.
"Yeah. Are you here to arrest the Team Rocket scum?"
"Actually, Agent Looker of the International Police will. I'm just here to represent my own agency and aid in any battles, but you seem to have that handled." Lance replied, observing the prisoners in approval.
"So, Harry, why did you attack Team Rocket's HQ?" Looker asked, though he wasn't angry, but merely intrigued about Harry's motives.
"My father, the Viridian City Gym Leader is its leader and tried forcing me to join him with a Psychic Pokemon... a clone of Mew. I had hoped that my father would change since age five, but that destroyed my hope, and when I heard that he was plotting to capture and interrogate me about Mewtwo, I trapped him and captured him, and destroyed his base after copying key information such as client lists, agent lists, bases, projects, bank accounts, and locations of evidence." Harry said, impressing Looker and Lance.
"What happened to the Mew clone?" Lance asked.
"Well, despite him using it against me, he hadn't actually caught it, so, once I defeated it, I caught it in a Master Ball and tried befriending him. That didn't work, but the actual Mew found us and took him under its wing. So Mewtwo is with one of the few Pokemon who can easily defeat it and should be contained as a threat."
"Good. We'll take your word for it. It's unlikely that we could do anything to him anyway with Mew and its clone as potential enemies if we tried." Looker said, though he wished to question Mewtwo and hopefully get more information on Team Rocket, he wouldn't push the matter. Harry had given them their best progress yet in defeating Team Rocket and deserved some trust. 
"Anyway, we can take the Team Rocket people into custody."
"Good. I was just gonna give them to Officer Jenny and attack Team Rocket's Academy next. What about the Pokemon liberated from HQ? I kinda feel responsible for my fathers Pokemon, but if they were stolen...."
"It will depend if they were stolen or poached. If your fathers Pokemon were poached, then they can decide where they go, but, if stolen they will be returned to their owners." Looker replied, and Harry handed him his fathers Pokemon, which a nearby agent scanned the Pokemon. 
"Surprisingly none were stolen; at least not according to our databases." Looker returned the Pokemon to a grateful Harry.
Harry let them out and asked them if they wanted to come with him or be released into the wild... they were all eager to be with such a kind trainer and made that obvious. Harry had treated them very well when he was young and he had a kind soul and didn't abuse Pokemon. Harry returned them to their Poke Balls and had Alakazam take them to his private island and then come back, Harry would let them out and tell them the secret later.
"Well, I hate to be rude, but the Indigo Plateau Conference starts in two weeks, and the Academy and Celadon Game Corner both need to be dealt with. I'm sure the International Police will be taking over, but you should let Lance or myself deal with the Executives and Vicious. One of them is my mother and I would love to put her in prison... two of them are Will and Karen of the Johto Elite Four." Harry said, to Lance's anger.
"I'll deal with those two traitors." Lance said angrily. Looker nodded in agreement, knowing better than to try taking two members of the Elite Four prisoner.
"I can deal with the executives and Vicious," Harry said. "I'm familiar with their talents and tricks. I just need agents nearby to take them into custody."
"That is easily doable," Looker agreed.
-----------------------------------------------------------------------------------------------
The executives Proton, Petrel, and Archer were all easily defeated by Harry and taken prisoner. Team Rocket's Academy was quickly taken with Harry having lured them into battle and sent his Charizard to use Blast Burn on their Pokemon. Team Rocket's secret agents were all exposed and thousands were taken prisoner and even more Pokemon were freed. Harry personally ordered Team Rocket's Academy be leveled and his Pokemon were all to happy to carry out the order. Harry just had his mother to deal with....
His had father impregnated one of his executives twelve years ago and Harry was the end result. She didn't write, send birthday cards, say I love you, or give hugs. Naturally, Harry felt cheated twice over in the parent department, and would be all too happy to throw her in prison. At least his parents in his first life actually loved him!
"Hello, Ariana," Harry said coldly, having taken her prisoner when she fled.
"What? Not happy to see your mommy?" Ariana asked mockingly. "I heard that you turned against your family... stupid boy. You could have ruled the world!"
"Nonsense," Harry said dismissively. "Team Rocket would face rebellions, insurrections, and generally be opposed at every turn. It was always doomed to fail. Goodbye Ariana." Harry said, walking away and letting the International Police agents take her.
Vicious was dealt with quickly, Harry broke his Dark Balls and took them for study and then caught himself a newly freed Sneasel and Scizor.
Eventually, Harry decided that it was time to apprehend his grandmother who had been attempting to recruit survivors to rebuild Team Rocket under her leadership. Harry was joined by a concerned Lance, who was eyeing the fifty Team Rocket people with apprehension.
"I'll handle the fifty trainers Lance. All I ask is that you don't leak my secret weapon for the Pokemon League and let the other competitors and Elite Four prepare." Harry said with clear confidence. His confidence was great enough that Lance felt no reason to doubt him, and indeed it reminded him to ask Harry a very important question....
"Harry, there are two vacancies in the Johto Elite Four and I've been allowed to offer you one of them." Lance said, though he knew Harry would likely refuse. "You've proven yourself to have a naturally very high level of skill and I can help you refine it to its full potential."
"Sorry, but no. I'm aiming to be the Kanto Champion, but I need the other leagues as my back ups." Harry replied. Though becoming a member of the Elite Four would help him get closer to being a champion, Harry wanted to take the long road, at least until he was an adult and needed to settle down. Harry had no desire to be an absentee father and not even the prospect of growing more powerful was enough to persuade him otherwise.
"I had to offer. You made the right choice though, at least in my opinion." Lance said. "Now, lets see that secret weapon you claimed to have."
"Happily, but I'll need to call out Charizard for this. It's a team effort." Harry said, before revealing himself to Team Rocket and calling out his Charizard. "Charizard! Mega Evolve!" Harry said, confusing his enemies and Lance. Confusion turned into shock as power emitted from Harry's Mega Ring and Charizard and light enveloped Charizard as he evolved into his Mega-Evolved form.
"Now.... Blast Burn!" Harry ordered and Charizard quickly defeated dozens of Pokemon with his most powerful attack. Harry noticed some nearby Pokemon moving in to attack and had Charizard use Hyper Beam and then defeat the rest with Dragon Claw and Flamethower. "What do you think, Lance?" Harry asked with a smirk.
"Impressive! I didn't even know that Charizard could evolve further!" Lance replied in awe.
"It's temporary and once per battle, but Charizard evolved into a Dragon and Fire type." Harry said, as Team Rocket was taken into custody by the Internation Police, and Harry and Lance were walking to his grandmothers front door. Harry had Charizard knock the door down.
"It was unlocked!" His grandmother screeched in anger.
"And the door handle wasn't booby-trapped?" Harry asked, causing his grandmother to suddenly become silent.
"Not with anything fatal...." She eventually replied, getting a glare from her grandson.
"You're under arrest." Harry replied drolly. "And I'm gonna break more of your stuff."
"You do realize that you're just destroying your own property, right?" Lance asked in amusement, getting a confused look from Harry. "The Pokemon G-Men and the International Police are letting you keep Team Rocket's legally owned properties like the Celadon Game Corner, your family's homes, and Pokemon Land; which was previously destroyed. This is a thank you gift and spares both agencies some paper work and hassle."
"Well, at least I didn't destroy a lot of my new stuff." Harry said as his grandmother was placed under arrest and led away in chains.
That seemed to have closed story of Team Rocket and Harry briefly returned to his private island to relax before the Indigo Plateau Conference. Harry was now a new billionaire and had the Celadon Game Corner making him millions a year and a theme park that was only good for scrap metal and real estate. Harry had also inherited several hundred million in rare art and would be selling a lot of it. Harry didn't have such expensive tastes and regarded it all as meaningless. Harry also kept around one billion of his fathers money before he knew that he would be legally keeping some assets, but the rest of Team Rocket's assets, some fifteen billion, was donated to several causes that bettered the lives of Pokemon and protected them from poaching.
Harry also set up mines for the precious metals and gems, and would be using the caves as habitats for the Pokemon who would eventually begin inhabiting the island. Harry was also pleased that he would soon be a multi-billionaire. Harry also had the extinct Pokemon restored from their fossils and established a habitat and breeding center for them.
-----------------------------------------------------------------------------------------------
Harry was among the first to register for the Indigo League competition and was eager for it to finally begin.
"I will win this. I have to." Harry thought, looking at the stadium. "All of my dreams hinge upon me winning the Indigo Conference and gaining the ability to challenge the Elite Four and Champion once I'm finally ready."
==Author's Note:==
For the purposes of my story, Will and Karen will both be the Johto Elite Four members with two unnamed members also in the group, with Lance as the Johto Champion. To become Champion you have to win the tournament, then defeat each Elite Four member in succession and defeat the Champion. Or be a member of the Elite Four and challenge the champion. The Kanto Elite Four won't be affiliated with Team Rocket, there just aren't enough replacements to go around, and doing so would damage any future plots of mine.