Prologue (Three Years Prior)

"Now I see what I have truly done, Red. You have shown me Lance's true intentions… I never thought that my greed would allow this much damage to occur. I will disband Team Rocket as best I can, but I do not control its entirety. I can only try…"

"No!" shouted Red. "You will destroy Team Rocket! You owe me this much, Giovanni! I nearly lost my arm to save you, and then you betrayed me! If it wasn't for Blue, I would kill you… but he says you have someone that you have to protect. I know how that is, and I also know how hard it is to get by without a father, so I'll leave you. But promise me that you will make sure that Team Rocket never takes another life! My father, my brother… and nearly my mother! Blue's family! The people of Cinnabar Island! All the Pokemon that you've slaughtered! And her…. I spent two years healing while everyone thought I had died! She died trying to avenge me WHEN I WASN'T EVEN DEAD! All of this because of YOU!"

"Red… I know your pain. When I was a child, my family died when the Celedon Game Corner's construction site collapsed. I went into denial… my first Pokemon was stolen, my family gone... I had nothing left. When I finally found the thief, he nearly killed me, but my Gardevoir… my last Pokemon... she saved my life at the cost of hers. Completely grief-stricken and enraged, I killed the thief and took his Pokemon, and, locking my memories away, joined Team Rocket. In a few years I was at the head of the organization's Kanto sect, and you came along. After all you did, it took you defeating me here to realize what I've become. Here, take this… it will allow you to disengage the barrier around the Indigo Plateau. That is all I can offer at this point…."

***

Chapter One

The Journey Begins

(Present Day)

Gold watched the waves roll by the side of the ship. He had turned thirteen on the trip to Johto, and he wanted to get his first Pokemon, right NOW. Gold and his mother were moving from Hoenn and its rising criminal population to Johto, so that Gold could start his adventure in a safer place. They were heading to the port in Cyanwood City, then taking a ferry all the way to New Bark Town.

Three hours later, Gold stepped off of the ferry and into New Bark Town. He knew from the maps he had studied on the boat that Johto, along with the region to the east, Kanto, made up the Indigo continent. He knew that the first town he would visit on his journey would be Violet City, which also held the first gym. And finally, he knew that the Indigo Plateau was across the Mount Silver. He was ready to sprint straight towards the lab he could make out at the other edge of the small village when his mother yelled for him to help unpack.

"Great," Gold thought before checking his watch. "Nine at night and I have to help my mom unpack everything we own. And the lab closed an hour ago…"

---

The next day, Gold got up and grabbed a pair of cargo shorts and a white shirt from his suitcase, one of the only things left unpacked because he was going to leave soon. He didn't even bother to comb his hair, so his hair was a mess, especially one bang that kept going into his face, so he put a hat on. He grabbed two extra sets of clothes to stuff in a backpack and slipped on a hoodie with his own design on it, a present from his uncle. Rushing out past his mom, he went straight over to the Pokemon Research Lab, headed by Professor Elm.

"Well, hello there," said Professor Elm when he saw Gold. "You must be Gold, the new boy from Hoenn. I understand that you are thirteen, so go ahead and choose a Pokemon; Chicorita, a grass type, Cyndaquil, a fire type, or Totodile, a water type. Choose quickly, though: today is Crystal's birthday, and I'm expecting her soon."

Gold thought about it for a minute: he knew that fire types were strong, and if you trained them enough, even water types were easy to defeat. But water types were notoriously fast, and Totadile's evolutions were very strong. And yet, grass types were balanced, and they could heal themselves. Just as Crystal came in, Gold picked up the Poke Ball for Cyndaquil.

Crystal was dressed in shorts, a tank top, and a light vest. Her blue hair was a mess, and she looked like she had just woken up, but was wide-eyed and on edge.

"Hey, Professor Elm," Crystal said. "And you must be… Gold? Yeah, that's it. Huh? You got your Pokemon? Please tell me you didn't take Chicorita!"

"No, I chose Cyndaquil, don't worry," replied Gold.

As Crystal picked up Chicorita, Elm said, "Why don't you give them nicknames?" Gold thought that it was a great idea, and nicknamed Cyndaquil Flare. Crystal decided not to nickname her Chicorita. "Now," said Elm, "could you take this Egg to Professor Oak? He's on the trail north of here. He might think this is interesting, as nobody has seen a Pokemon Egg quite like this one."

Gold and Crystal accepted, but as they were at the outskirts of the village, Gold's stomach growled.

"I forgot breakfast!" he said as he ran back home, leaving Crys laughing before her own hunger hit her.

Thirty minutes later, they left, both set for the journey they were setting out on.

"So you want to be a battler, Crystal?" Gold asked as they walked.

"Please don't call me Crystal. I never liked that name… people usually call me Crys, probably because I'm a tomboy. But no, [I]my[/I] goal is to become the world's most renowned natural Pokemon Professor. I want to find ways to help the environment using Pokemon that want to help me. You see, my father was poisoned by toxic sludge at a factory that was polluting the environment. I fear that one day, I'll get a call from the hospital that he didn't make it…"

"Oh, sorry…" Gold apologized. "Well, I want to be the first person to go to all five known regions- Kanto, Johto, Hoenn, Sinnoh, and Orre- get all the badges, and win the Indigo Rivalry, the Silver Conference, the Ever Grande Championship, the World Battle, and the Shadow Tournament, respectively."

At this, Professor Oak's cabin came into view.

"Race ya," said Gold, and the duo was off.

As they knocked on the cabin door, Professor Oak answered and let them in. After an hour of lecturing about Pokemon, how to catch them, where they lived, their individual personalities, and something about youngsters not knowing how much they have it made, Gold and Crys slipped out with the Pokeballs that they were given during the "how to catch them" part.

"At least now we have some Poke Balls, and we know the path to get to Violet City," said Gold. "That's were the first Gym is."

"And," replied Crys, "Sprout Tower is located there, too. It's renowned around these parts for being a guardian of the city."

As they approached the Violet City Gates, a Ledyba appeared out of the grass.

"Sweet, some training!" Gold yelled as he threw Flare's Poke Ball.

As Flare appeared, he yawned and lay down. The Ledyba noticed them now, and tackled Flare. As Flare flew backwards, he somersaulted mid-air and sent a small stream of fire from his mouth, badly burning the Ledyba. Then, Gold threw one of his empty Poke Balls at it to capture it. As the ball rolled back and forth, Gold knew it could pop open and break the Poke ball. After a few rolls, it stopped, and Gold knew he had caught his first Pokemon.

"Oh, yeah, Ledyba is mine!" Gold yelled. Then a thought occurred to him, and he said, "Actually, I'll call it Ledya. I'll nickname all my Pokemon."

As they walked into Violet City, they were astounded. Gold had grown up in Littleroot Town, with about thirty other people. Crys had grown up in New Bark Town, with only seventeen other people. But Violet City was huge compared to them. It had over 150 people with over seventy Pokemon, plus all the bird Pokemon living above the city and the Bellsprout in Sprout Tower.

Then there was the Gym. When it came into sight, the Gym Leader was performing on the roof with his Pokemon. Pidgeotto, Murkrow, and Staravia were all there, and the Gym Leader was riding them, jumping from one to another as they flipped and did stunts. Then, they all used Ariel Ace, flying at Mach 1 in a circle, and Gold knew he had no chance against such fast Pokemon.

"I need to train first," he thought before saying, "Let's go to Sprout Tower."

As they wandered around the city, it came into view: ten stories tall, covered in greenery, and rocking gently. He knew it was the perfect place to train.

When they got inside, Gold went off and said he'd return at dusk, leaving Crys to study to "Bellsprout Pillar", the supporting column in the center of the tower. Legend had it that a hundred-foot-tall Bellsprout had been the protector of the city in feudal times. When it was badly hurt by a bewitched Entei, the Entei broke the spell and granted the Bellsprout one wish. The Bellsprout wished to be a monument to peace, and was transformed into the tower's pillar. Entei then told the city to build a tower around the pillar so that they could fulfill the Bellsprout's wish, and be protected by it.

She decided that she needed a better look, so Crys went up a few floors. While she was climbing the stairs, a Bellsprout appeared and attacked her!

"Go! Chicorita!" yelled Crys as she threw Chicorita's Poke Ball. When Chicorita appeared, she used Razor Leaf to attack the Bellsprout, who countered in the same way, sending sickle-shaped leaved toward their opponent. When the attacks collided in midair, the Bellsprout released a cloud of orange powder and blew it towards Chicorita. Chicorita then used Razor Leaf to reverse the direction of the powder and tackled Bellsprout. As Crys was about to throw a Poke Ball at it and capture it, the Bellsprout spit a purple substance at Chicorita, and Leaf turned white and froze. Chicorita turned to see what was wrong, and Bellsprout attacked her. All of a sudden, an old man appeared and calmed the Bellsprout.

"Who might you be?" the old man asked. "And why did you just attack a Pokemon from our tower?"

"Bellsprout attacked me," explained Crys, "so my Chicorita attacked it. Then it used a purple a-attack…" She froze again.

"What is wrong?" the old man inquired.

"Th-the poison… not poison…" Crys calmed herself before explaining. "I want to help clean the world up from pollution because my father was poisoned, and I want to let him see a cleaner world when he wakes up. But poisons scare me horribly bad."

As the old man nodded, the Bellsprout Pillar started to rock back and forth. Then Crys heard Chicorita say, "It's true, I promise."

"Did you just speak?" Crys asked, bewildered.

"Yes, your Chicorita has spoken. You have been granted this by the Bellsprout that became a pillar. He sees you as a worthy person," the old man said, and left.

---

Three floors up, Gold sent Flare and Ledya out of their Poke Balls. He went around the floor and gathered about twenty Bellsprout and said to them, "I need to train for the Violet Gym battle. Would any of you like to help by battling my Pokemon, Flare and Ledyba?" At this, the Bellsprout began to nod slightly. "Thanks, we can do one-on-one battles. Who wants to go first?"

A few Bellsprout stepped forward and assumed fighting stance. For the next hour, Gold trained his Pokemon, having Flare use Ember and Ledyba using Comet Punch and Gust when, after a battle with a particularly feisty Bellsprout, Ledya evolved! As he glowed, some Bellsprout seemed to smile. Then, all of a sudden, there was a Ledian!

"Awesome, Ledya evolved!" Gold yelled.

Then an old man appeared. "You revel in fighting, and are joyous when someone becomes stronger. Why?"

"I want to become a great Pokemon trainer," Gold said. "I asked the Bellsprout if they could help me with the first step, the Violet Gym, and they agreed to help me by battling. They even smiled when Ledian evolved!" Gold answered.

"Very well…" the old man said.