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"Once again, I apologize for my part in the assignment, but I didn't expect at the time that all this would have happened. Besides, between refining the practice of genetic augmentation and planning my own escape from my contract with Giovanni, I wasn't really in a position to keep track of her, nor did I understand she would be used in this manner."

"Alright, alright, I accept your apology. Now how much longer will it take?"

"I'm just about finished."

Rue watched over Martel as she treated Felicia to rid her of the mind control or whatever Black IX really was. She didn't exactly know what she was looking at. Martel might as well have been a Martian prodding her with alien devices. The standard conventions of surgery and medicine didn't apply with the kinds of advances she made while working for Team Rocket. She mentioned surgery at the start, but never once did she even pick up so much as a butter knife. Hell, Rue didn't even know if she was using anesthesia, or if it was even applicable here.

Martel put down the last instrument and took a step back. She let out a sigh of exhaustion, having operated on Felicia on and off for the past twelve hours. What exactly she was doing was a mystery to anyone who wasn't savvy on her knowledge of medicine, but the closest she could describe it was like trying to restructure a Jenga tower the size of a small office building brick by brick.

A few minutes had passed, and finally Felicia stirred. She moved to sit up, her hair slightly dissheveled. The first thing she noticed were the many wires and monitoring devices strapped all over her body. She then looked up at Martel and Rue in bewilderment.

"Martel? Rue?" she asked. "Where are we? How did I get here?"

"We're back in Hoenn, Felicia." Rue replied. "Do you remember what happened?"

Felicia opened her mouth briefly, her eyes followed the motion, and she let out the sigh of someone who just realized their dark secret had just been discovered.

"Yes, sir." she said. "Look, I just want to-"

"Hold that thought." Rue turned to Martel. "Wait outside."

"Alright, sir, but don't do anything stupid. She's still a patient in my care, and I won't have you manhandling my patients!"

"Just... wait outside!" Rue repeated. Martel huffed and left the room, leaving the two of them alone in the room.

"Sir, I'm sorry I didn't tell you about Black IX." Felicia explained. "But I was programmed not to."

"I get it, you didn't have any choice." Rue sighed. "Honestly, if it was anyone else, I'd probably be a lot angrier. Right now I'm, though, I'm more relieved than angry. You... I... you help manage the base. I'd hate to lose you."

"Thank you, sir." One by one, Felicia removed the various wires and monitoring devices strapped to her body. "How long have I been out?"

"Just over a week. Shit's been getting real ever since Giovanni captured Mew."

"So we lost?"

"Almost. We barely escaped with our lives. Turns out he has a trump card of his own: a Mega Tyranitar the size of a Wailord. I guess he's got his own team of labcoats working with the information Martel left behind to supercharge his Pokemon. Now he's looking to take over the Pokemon League and the world government. If they don't surrender to him, he'll annihilate the Indigo Plateau."

"So this is where it all begins... and ends." Felicia said. She attempted to climb out of bed, but she nearly fell over, given that her legs went unused for over a week. Rue caught her and helped her stand. There was something really wrong seeing Felicia like this. She was always so unflappable; seeing her struggling to stand was a highly disturbing omen to Rue.

"What are we going to do, sir?" she asked.

"Well we're still alive, and if Giovanni conquers the world, there won't be a safe haven for us. For anyone, really, who disagrees with him."

"And how do we plan to deal with a Mega Tyranitar? Alakazam can't lay a finger on him."

"I don't know. I'm still trying to figure that part out."

"I take it Mewtwo will be helping us?" Felicia asked.

"Actually I don't think... he's in any condition to help us." Rue replied hesitantly.

"What happened?"

"Mega Tyranitar tried to vaporize us with a more powerful verion of the Hyper Beam. The devastation it wrought was... beyond awesome. We were right in the line of fire, but Mewtwo... he appeared before us to deflect the attack long enough to teleport us away; you, me, and Jessie. I haven't seen him since, and there's no way he could have survived the blast. We can only assume the worst."

"Why did he save us? He hated us."

"I guess because he figured we had a better chance than the Pokemon League at stopping Giovanni. Maybe he's just using us for revenge for him capturing Mew? Who's to say? I sure as shit am not doing this for his sake! Giovanni fucked us over, tried to kill us, manipulated us, manipulated YOU, and now he's threatening to blow up the League. He's going down, and we're gonna throw everything we have at him!"

"And how do you plan to do that, sir?" Felicia challenged. "With everything you told me, it sounds like we're horrendously outgunned, more so now than last time because we won't have Mewtwo with us."

"What's our alternative, Felicia? Run off and hide in some abandoned corner of the world as he accumulates more power and takes it through military strength? If we're going to strike, we need to strike now, before he becomes truly unstoppable!"

"Fine. Whatever you want, sir, I'll follow."

"You plan to storm Giovanni's HQ?" Martel asked from the doorway. Rue and Felicia turned to face her as she reentered.

"Will you come along, too?" Rue asked.

"Not sure. I still have my clinic here that I need to run. I'm a doctor, not a fighter. You want me to boost your Pokemons' performance, do a nip/tuck, swap out body parts, I can do all that. A Pokemon war, that's a bit too far out of my pay grade."

"Shame. We could really use another Trainer."

"You have a crew of over seventy. How many more do you need?"

"Not all of them are coming with us. The new tilt-rotor isn't large enough to hold the entire crew compliment, and we need someone to take care of the slaves and the base."

"Ah, right."

"Come on, Felicia. We need to get ready."

* * *

The new tilt-rotor was a hell of a lot faster than the zeppelin. They soared over the Hoenn region, heading east until they hit the sea. They continued eastward from there for a while before moving off to the north. For almost half an hour, the ocean was completely featureless. It was both beautiful and slightly terrifying, for the other side of that realm was completely inhospitable to their kind. Rue didn't like the sea for that reason; just the thought of getting stuck out in sea with no means of escape was a worse fate than death.

Finally, they spotted Cinnabar Island appear on the horizon. From there, they headed North to the mainland of Kanto. It was another stretch, albeit a much shorter one, of ocean before the mainland appeared. It wouldn't be much longer before they reached Viridian City, and Team Rocket's HQ located on the outskirts of the city.

The tilt-rotor was piloted by Asellus, a crew member who worked as an airline pilot before she was recruited by Rue, and piloted the zeppelin before it was destroyed. The other members of their team that came along for the final battle included Felicia, Emelia, May, Misty, and several other crew members. All of them were equipped with six Pokeballs each; sixty six total, minus Asellus, since she'd be busy piloting the ship.

They passed over the plains south of Viridian, which eventually broken by the thicket of forests that the region was known for. They passed over the entire length of the city in a few minutes, and from there, Asellus turned the ship to the north east, where the forest butted up against a large mountain range in the distance. When they neared it, Rue could make out the fortress that was Giovanni's HQ sprouting out from among the treetops. The closer they got, the further away from the fortress those trees got until there was a solid mile between them.

"Do you have a plan of attack?" Felicia asked Rue.

"I have no idea. We can't really plan our assault until Giovanni gives a response to our arrival."

"So we're just going off the cuff?!" Misty exclaimed.

"It's all we can do at the moment."

"Looks like we won't be waiting around for long! Brace yourselves!" Asellus shouted, then banked hard to the right. A column of light shot past them, and Rue felt herself nearly become one with her seat from the whiplash. They relevelled, and down below, there were several flashes of light as numerous Pokemon appeared. At the forefront of the entire contingent was the Mega Tyranitar.

"Holy crap, we have to go through that?!" Asellus whispered.

"Just stay out of its line of sight." Rue explained. "If it begins charging up energy, MOVE YOUR ASS."

"Alright. Then how do we destroy it?" Misty asked.

"I have no idea, but if we can get inside the fortress, I don't think Giovanni would be insane enough to fire its Ultimate Hyper Beam at himself."

"Wait, did you say Ultimate?" Misty asked.

"Alright, it's time for us to make our move! May, light up whatever grass-types you see on the ground, make a pathway for Misty. Misty, you have the ice. Ground the flying fleet any way you can. Asellus, keep the ship far away from the battle. Emelia, you keep the ship safe from enemy attacks!"

"And what about me, sir?" Felicia asked.

"Felicia... protect the others. Keep an eye on that behemoth and make sure the others are safe."

"Yes sir." Misty and the other girls jumped out of the back of the tilt-rotor one by one. Emelia took flight on a Fearow, along with the rest of the crew members, and Misty and May parachuted to the ground. Rue moved to the rear of the plane with Felicia. She drew out her Pokeball when Felicia stopped her.

"Rue... wait." she said, grasping at her hand. "Before we go, just in case something happens to either of us, I just wanted to say... I love you."

Rue was taken back slightly by it, though she didn't show it.

"Mm... don't die, Felicia." she replied. Felicia gave her a quick hug then pulled away, preparing to jump herself. Rue watched her go first, summoning her Skarmory and flying out past them. Finally, she jumped, summoning her Pokemon, a Pidgeot, one that was quite a bit larger than its brethren thanks to genetic augmentation.

* * * Remove this

Rue ducked down as she saw a flock of Mega Pidgeot suddenly swarm in over her head, flying in perfect formation. They made a beeline straight towards Mega Tyranitar. As they leveled out, Rue could see Martel on the Mega Pidgeot leading the charge. The riders on the other Mega Pidgeot, she could identify some of them as Martel's assistants and apprentices.

The Mega Tyranitar fired pulses of dark energy at them, but they effortlessly dodged the attack. They returned to formation, with Martel at the front.

"Ready, team!" she called out. Each of the assistants, including herself, pulled out two Pokeballs, one in each hand. "Go! Electrode Explosion Barrage!"

They all threw out the Pokeballs, which all released Electrodes primed to detonate even before they even fully formed out of the light. They shot down like missiles at the Mega Tyranitar and all detonated on contact. The combined might of all the Electrodes, who were no doubt genetically augmented, caused the Mega Tyranitar to stagger back. Its foot dug up giant fissures in the ground as it recoiled from the attack. When the smoke cleared, Rue could see cracks had formed across its entire body, but it was still standing, if just barely. It brought its head up and opened its mouth at Martel and her team. It began to charge up energy for an Ultimate Hyper Beam. However, this didn't faze Martel, and she drew out another Pokeball.

"Oh no you don't!" she shouted, then threw the Pokeball out. "Mega Electrode! BIG BANG!"

Rue didn't see what Mega Electrode even looked like as it was still engulfed by light when it disappeared into Mega Tyranitar's mouth. It paused in shock as it realized it swallowed a Pokemon. Light then poured out of all the openings in its body, from its mouth, holes, and cracks, and its form exploded with enough force to create a visible shockwave. It bowled over all the trees for hundreds of yards around, and appeared to also disable the fighters on the ground. Pidgeot squacked in shock and tried to compensate as the wind was knocked out from under its wings, and they tumbled down several meters before he was able to catch the air again and maintain flight.

"What happened to not getting involved?" Rue asked Martel as she flew over to her.

"I had a talk with the staff, and we had a change of heart." Martel explained. "If Giovanni takes over the world, we won't have anywhere to hide, so we're fighting now to maintain our freedom."

"Hmm. Well, thanks for the change of heart." Rue replied.

"Better move along, sir!" Martel said. She looked towards the fortress, where there was another flash of light. A massive Gyrados, much larger than they grew in the natural world, came flying out of the light, mouth open wide enough to devour an entire school bus without notice. "We'll keep them busy. You get to Giovanni!"

Martel and Rue both dove at the flying dragon. Martel's staff joined them in formation. As they reached Gyarados, they broke away and scattered in all directions. Rue missed its maw by several yards, banking to the side to glide along its edge. The Gyarados roared and wheeled around to pursue one of them. Fortunately for Rue, he took the bait and chased one of Martel's staff.

With Gyarados out of the way, Rue continued to make her descent on the fortress. Pidgeot tucked in his wings and went into a dive bomb, closing the gap between them and the fortress faster than before. There were still a few Team Rocket grunts behind the walls. When they were a hundred feet over the ground, Rue rolled off Pidgeot's side and grabbed his talons. Pidgeot buffeted his wings and acted as an ad hoc parachute. With just ten feet left before they hit the ground, Rue let go and stuck the landing. She already had a Pokeball ready when she hit the ground, and tossed it out, summoning his Alakazam. They were immediately bombarded by attacks from all sides, but were protected by Alakazam's barrier. With a gesture of his hands, the enemy was thrown back, Trainer and Pokemon alike.

Now that they had a moment to look around, there didn't seem to be anyone else in the fortress. The main structure towered over them, nearly a dozen stories tall. It was a very featureless and angular structure; more like an office building than a fortress, though there were no windows to speak of. Its design was inspired by medieval castles, but without many features or details, it looked more like a mass of metal spikes jutting out of the earth.

Rue led her Pokemon to the front door, where she summoned her Rhydon to bust it down. It took him a few tries, but after the third ram, the giant steel doors gave way and exploded inward into a cloud of twisted metal. The interior of the fortress was well lit by lights on either end, providing nice even lighting down the entire length of the corridor that stretched out before them. It almost reminded Rue of her own base, but it was at least designed with comfort in mind. This place was hostile both inside and out; that was probably the intention.

They moved down the corridor to the far end of it. The walls were far enough apart that several vehicles or large Pokemon could move side by side with elbow room to spare. There were doors on either side of them leading to different parts of the base, including blast doors like the entrance. Since there was nobody else around, Rue assumed they were not prepared for a full on invasion. Maybe they assumed the giant Pokemon would have sufficed?

The group approached the end of the corridor. The room beyond faded into view to reveal a large arena, similar to the one found in any Pokemon Gym, but specifically, the one in Viridian City. The steel floors in here were substituted by a flat dirt turf. On the other end of the arena stood Giovanni.

"You are remarkably tenacious." he said as they approached.

"You made me that way. You only have yourself to blame." Rue replied. "So why try to have me killed? Why shut down my operation? You invested a hell of a lot of money and your own blood and sweat to make me the woman I am."

"You were no longer needed." Giovanni began to pace back and forth across the arena slowly as he explained. "When I first took you under my wing, I expected you to be my protege; my successor. You were reckless, though; reckless, insubordinate, and you were quickly proving to be a liability for Team Rocket. Then... I found that I no longer needed you. I just needed Black IX and Jessie."

"Felicia." Rue corrected.

"Black. IX. You were simply borrowing her until I needed her."

"To kidnap Jessie."

"Whatever I needed at the time. When I tried issuing her orders, however, I discovered a strange amount of interference. Coming from you."

"Martel told me."

"You're more disruptive than I ever imagined possible." Giovanni glared viperously at Rue. "It seems to be in your very nature, and I plan to rid myself of this disruption right now, once and for all."

"You're annoying to listen to. Alakazam, flay his mind." Rue commanded. Alakazam fired an invisible wave of psychic energy at Giovanni, but there was no visible effect on him. If it wasn't for Alakazam leaning his head forward, focusing his abilities, she would doubt he was doing anything at all. Giovanni flashed a crooked smile, then, with a sweep of his hand, fired a huge wave of dark energy that blew everyone - Rue, Pidgeot, Rhydon, and Alakzam - into the opposite wall. Rue slumped to the ground, dazed and utterly confused.

"What the fuck?!" she groaned as she stumbled to her feet. Alakazam quickly sprouted to his feet and threw up a barrier around them as a column of fire suddenly jetted out at the group. Rue shielded her eyes from the blinding light. Once the flames died down and her eyes readjusted to the relative darkness, she scanned the arena for where the Pokemon that fired those blasts was hiding, but aside from her own Pokemon, there were no others. The only one who could have done it was...

"Did you like that?" Giovanni asked. He demonstratably held his hand up and formed a fireball between his thumb, index and middle fingers.

"What the fuck..." Rue repeated. "What are you?"

"I am Giovanni, and this that you see is the ultimate conclusion of all genetic augmentation!" Giovanni let the flames spread across the rest of his body in an even grander demonstration of his power. "Your ambitions, boy, were too narrow. I always kept my eyes on the bigger picture. Every genetic experiment - you, your Pokemon, Black IX - were just steps to this ultimate conclusion! But... to complete this process, I had to have the one Pokemon, the master key to the entire genetic library!"

"Mew." Rue finished for him.

"So Julian told you? Yes, I know he changed his gender when he escaped, but I kept tabs on him ever since he left. I thought it would be useful to know what he's up to and let him believe that he escaped.

"And now you delivered yourselves to me. I may not have the Master Project anymore, but I have something even better: the power of a god!"

"Everyone, attack!"