Chapter 1

A lone man climbed the side of a mountain. On his shoulder rode a Pikachu, who observed its Trainer's damaged form. A scar was down the left side of his face, and blood was oozing from the side of his mouth. The man's legs, although they were covered by a pair of jeans, had many bruises, and his arms held many more.

"I…still can't believe I failed…" Red murmured as he hauled himself onto a ledge. He sat there, panting, as Pikachu leaped from his shoulder to check out the surroundings. Team Rocket had recently swept through the area and captured the majority of the Pokemon. Those that were left were in hiding.

"What can I do now?" Red said, mostly to himself. "The Gym Leaders and Elite Four are dead, and…and Leaf is now a Team Rocket Administrator. There's…there's no hope, is there, Pikachu?"

The little Pokemon put a comforting hand on Red's knee, smiling. It then leaped onto Red's shoulder as he began climbing again.

Recently, Red had been imprisoned in the Saffron City Kanto Prison after he had refused Giovanni's offer to join Team Rocket. He had been awaiting execution, his Pokemon held in suspended animation, when Sabrina appeared. She was among the last of the Gym Leaders, and had rescued Red and his Pokemon, ordering him to hide in Mount Silver. Red had done just that, evading Rocket hunter-killer teams and even fought Leaf near the Victory Road.

The battle had been harsh, but Red had prevailed. Leaf stepped aside and allowed Red to escape, saying that she might not be so merciful next time.

Red paused at the top of Mount Silver, where he could look over both Johto and Kanto. He had been here for a year before Gold and his team defeated him and sent him home.

"We're going to be spending a very long time here, pal," Red said to Pikachu. "We might as well get comfortable."

Twelve years later…

A young boy stretched as he exited his home in Pallet Town. The sun was rising as Team Rocket soldiers marched through the roads. There weren't a lot, just enough to make sure that no rebellions or riots formed here. They were still threatening, though.

The kid, whose name was Brad, wore a pair of black shoes and jeans, with a white shirt and a red and black cap styled somewhat like a PokeBall. He had green eyes, brown hair, and stood at about five feet, seven inches.

Several kids were playing nearby when one of them ran into the street and collided with a Rocket soldier. Brad decided to watch what was to happen.

"Oops! Sorry mister!" the kid said, smiling.

"You little prick!" the Soldier shouted, grabbing the kid's shirt and lifting him off the ground. "You dare run into me? A member of Team Rocket?"

The kid's eyes were filled with confusion and fear. His friends were too afraid to move, even think. Suddenly, a woman flew out of the door to a house, a Delcatty right behind her. She raced to the Soldier and snarled, "Get your filthy hands off of my child!"

The Soldier growled and punched the woman in the face, sending her to the ground. The Delcatty hissed, arching its back, but then the Soldier sent out his Toxicroak.

"Make sure it does not interfere while I deal punishment to these…offenders," the Soldier ordered, turning his attention back to the child in his hand.

"As for you, you little shit…" the Soldier raised his fist and smashed it into the child's face. Tears began to well up in the child's eyes as the Rocket threw him to the ground. He glared at everyone, turned, and left, the Toxicroak following him.

Brad sighed; such things weren't uncommon. Several years back, he had been punched in the gut for simply getting in the way of a Rocket patrol.

Brad walked to the nearby forest, where he would always head off into when he wanted to be alone. As he wandered, he spotted Flying-type Pokemon flying through the sky. According to his parents, ever since Team Rocket came to power, the four regions of Kanto, Johto, Hoenn, and Sinnoh went under drastic changes. For one, the Pokemon League had been disbanded. There were no more Gym Leaders, Elite Four, or Champions.

Next, Trainers now had to be approved by defeating a Rocket Mayor, which were appointed to watch over their appointed towns and hand out PokeBalls and Pokedexes to new Trainers. Those who failed to defeat the Mayors could not be allowed to catch any Pokemon besides the one they owned.

Suddenly, Brad heard a faint moan from somewhere nearby. He raced through the trees until he saw an injured Bagon lying on the ground. It looked up at him weakly and cried out.

Brad gently picked up the Bagon and held it. It looked as though it had been beaten, but that didn't matter. He raced back to Pallet Town, avoided the Rockets on patrol, and entered his home.

"Mom!" he shouted as soon as he stepped into the living room. "Dad!"

His parents raced over from the kitchen. His father was about six feet, two inches tall, with dark hair, a hard jaw, and strong muscles beneath his black business suit. His mother was only one inch taller than Brad, with green eyes, an orange dress, and red hair. Both looked worried when they saw the Bagon.

"Where did you find that, dear?" his mother asked.

"Out in the woods!" Brad answered. "It's badly injured!"

"Alright, take it to the kitchen. We'll heal it up there," his dad said. "We have some medical supplies in the cabinet."

Okay, to clarify, this story takes place about twenty years after HG/SS. In case you're wondering, we will be seeing Unova and 5th Generation Pokemon, but not for quite a while. Team Rocket has not yet conquered it. Someone else has, but more on that later.

Also, here are the new ranks of the Team Rocket army after the conquest of the world:

Grunts-Same as the Games.

Administrators-Control the Grunts, but only have authority over small groups.

Executives-They control over all Administrators and Grunts. They have access to the Capitol Cities of Team Rocket in each region. However, they do not have as much control as…

Mayors-They have complete control of each city and the civilians and Rockets in them. They battle new Trainers to see if they are worthy of being able to travel and capture new Pokemon. However, some Mayors are given control over two cities/towns if one of them is too small for its own Mayor. An example is Viridian City-Pallet Town.

Presidents-There are a total of four, one to control each region. They are handpicked by Giovanni himself, and control every Mayor in the world. Only Giovanni commands them, and their Pokemon are extremely strong, so strong that only Giovanni can beat them in battle.

And…there you have it. Leaf will also be making an appearance in a later chapter, if you're curious.