View Full Version : [Pokémon] Pokémon: Johto Theory

October 17th, 2009, 7:34 PM

I was bored, and started writing this a few weeks ago. A few people liked it, nobody disliking it yet, so I decided to post it in here. By the way, this is my first Fanfiction, so please give constructive criticism and tell me what needs to be fixed.
I have a plan for Lugia and Giovanni later in the story. I think it's a good plan too.

Chapter List:
Prologue - No More Whirls
Chapter 1 - Two Journeys (http://www.pokecommunity.com/showpost.php?p=5232302&postcount=2)
Chapter 2 - Fate (http://www.pokecommunity.com/showthread.php?p=5232309#post5232309)
Chapter 3 - Team Rocket Returns (http://www.pokecommunity.com/showthread.php?p=5232319#post5232319)
Chapter 4 - Bad gets Worse

Pokémon: Johto Theory
No More Whirls

20 years ago, in the middle of the Whirl Islands area of Johto, an explosion destroyed The Islands, and Cianwood City, as well as blocking the ocean entrance to the area and severely lowering the water level all around the Whirl Islands by many hundreds of meters. This explosion had been caused by Team Rocket, who, after trying to catch Lugia, blew up the Islands on purpose, because they had failed. Giovanni had gone in to fight Lugia, fought him and lost, then ran like hell out of the cave as his Commander Apollo made a pokémon use Hyper Beam, thus causing the explosion that reformed the Island area and lowered the water level. This explosion caused panic mostly in Johto, but some heard it in Hoenn and Kanto, which caused small panic, because it was a large explosion. But for those close to it, it was disastrous. Many lost their homes and belongings, including pokémon of theirs, a small amount lost loved ones, and many water pokémon lost their lives. But of course, all that lived in Cianwood city died, most buildings were destroyed, and even including the Gym. The way this occurrence affected the Whirl Islands was even more catastrophic than that of the land mass, but less than Cianwood City’s damage, somehow. The Islands were mostly destroyed, yet, there were still a few caves around over the lowered water level; Lugia had protected his caves, and the Hermit that lived in the caves had survived, as well as Lugia. Since then, the destroyed parts of cities had been rebuilt, except Cianwood, and new cities had been built where the Water had been. Cianwood was a memorial site; they left everything there alone, as well as adding a stone that let people know who died on that fateful day. Happiness has returned to Johto and that event is not remembered by those Younger than 24.

October 17th, 2009, 7:35 PM
Chapter 1
Two Journeys

“This is a once in a lifetime chance!” thought Jacob as he shot through the Ilex Forest. The reasons for these things, him running, and his thought, were similar.

The reason he was running was because he ran out of the house when his bickering parents yelled at him. Since he ran out, and his parents didn’t call after him, they probably didn’t care what he did so he decided that he would travel the beautiful region with a Pokémon at his side.

Jacob was fifteen, he was not a spectacular sight, but people liked him for who he was, even adults looked up to him. He was 6’2”, tall for his age, had short black hair, green eyes, and he normally wore Jeans, a tee-shirt with a Pokémon logo, skateboard shoes and a sweatshirt.

Though today, since it was hot outside, he had worn shorts, no sweatshirt, and a Pokémon logo shirt.

He was one of those guys who acted all cool and such, but always stood up for the weak ones; he was nice to all but those not nice to others.

He had graduated from trainers school two years ago, and was able to catch and train Pokémon by Johto’s law; Though, he had decided to stay in town for a few more years before he ran off, but there he was, running.

Since he had graduated from Trainer’s school, when he bolted out the door of his home, a thought of happiness hurtled through his mind.

He was going to stop running when he got to Professor Elm’s lab in New Bark Town.

He was hoping he wouldn’t slam into any Pokémon on his way because it is likely they would attack him and he would be likely to get hurt.


Daniel had been having a good, calm afternoon, until some strange pokémon attacked him. He was now running from it, scared as hell.

Now, let me describe this pokémon, it was all dark, no color on him other than many shades of gray, a shadow Pokémon; New to Daniel and even Professor Birch, once he was told of it.

As Daniel was running, he tripped over a tree root, and nearly fell over a cliff that had a tree in the middle of the two sides.

“Whew, that was close.” Sighed Daniel, as he got up and brushed himself off. “Crud, it’s still following me, I'd better keep running.”

Daniel was also fifteen, almost sixteen, and had been on a journey for two years already; helping Professor Birch and Rowan find Team Rocket, having captured a few members.

He had a Poochyena that he had gotten as a starter, and had trained it up to a Mightyena over the past 2 years; sadly, he did not have any of his pokémon with him. They were at Birch’s Lab.

Daniel got to Birch’s just in time for this horrible thing; that I cannot tell you about yet. Anyway, Daniel got his Mightyena back, as well as 5 other Pokémon of his and then he and Birch left.

October 17th, 2009, 7:38 PM
Chapter 2

Jacob arrived at Elm’s lab by nightfall, but was not able to get in because they had closed it for the night.

Jacob sat around for a while before realizing Elm's house was right above the lab. As soon as he realized this, he ran up the stairs on the side and knocked on the door.

He waited for a while before he heard footsteps from inside and the door opened. As the door opened Jacob saw Professor Elm and the professor asked “Can I help you kid?”

Jacob answered with a simple “Yes,” then said “I would like to start my Pokémon journey. I just got here from Agnoviouex City when running all day.”

“Holy crud kid,” started Elm, “I wouldn’t have expected someone to run that far just to get a starter, and without anything to defend themselves with.”

“Well, it was more than that professor. I was running from home, and since I have my License to train Pokémon I thought I’d just come here so I could start my journey,” finished Jacob, “By the Way, my name is Jacob, as you didn’t already know that.

“Okay then Jacob, I trust you have your License and Trainer Card with you?” asked Professor Elm, “because if you don’t, I can’t give you a starter.”

“Of course. I carry them with me every day. I’ll just get them out.” Jacob says, then reached into his pocket expectant to find his Trainer Card and License, but only found old pocket lint. “Damnit! It’s not in my pocket. I must have dropped somewhere nearby, I’ll go look.”

“Hold on kid, are those two cards below your feet them?” questioned Elm.

Jacob reached down to pick them up and looks at them, says, “Yep, those are it.” then picks them up.

Professor Elm then said, “Jacob, since you seem to be ready for this, let’s go into the lab and see what Pokémon I have to offer.”

The two then went down the stairs and into the lab. As Elm turned on the lights, Jacob’s jaw dropped; the lab looked exactly the opposite of what he expected.

It didn’t look boring at all, there were cool looking machines all around, a pile of pokéballs was lying in the corner. The room was pretty stuffed, but felt empty.

Professor Elm walked over to the pile of pokéballs and started sifting through them. He then asked Jacob, “So, which pokémon were you hoping to get?”

Jacob started saying that he wanted a Cyndaquil, but was interrupted by Elm telling him that he could only have a Hoothoot.

Since it was his only choice, Jacob took the Hoothoot and thanked the professor. He was just about to walk out of the room when Elm grabbed his shoulder and pulled him over to a door in the back of the room.

As he was pulled through the door, he heard the noises of doors closing behind them then as soon as Elm stopped; they started moving down, as if they were in an elevator.

Suddenly, Professor Elm turned him around and he could see into an amazing looking underground building.

“This is Johto’s underground police agency,” said Professor Elm, “it’s been under my lab since a few months after the event in the Whirl Islands. It was built for the sole purpose of tracking down Team Rocket members.”

“I pulled you in here because you look like a strong-willed teenager,” Professor Elm said as they exited the elevator and started walking around the agency, “and we need someone like you to help us catch them while on your journey.”

“Sounds like fun,” Jacob said as soon as Elm was done, “when can I start?”

The two of them walked over to a room, Elm went inside and started talking to someone inside as Jacob waited outside.

Elm walked out followed by another man, tacking to him, and told Jacob, “Jacob, this is Professor Oak.”

“So, you’re Jacob?” asked Professor Oak, “How nice it is to meet you.”

Jacob first replies “Yes,” then said, “It is nice to meet you too. I often listen to your Radio show. It’s my favorite one from Goldenrod.”

“Well, you must be an avid listener then,” said Professor Oak, “anyways, as Elm has probably told you already, this base has been searching for Team Rocket for about 19 years.”

“The reason for searching for them is to make sure they go behind bars for what they did to nature 20 years ago.” Oak told Jacob.

“Professors Birch and Rowan are also working together in Hoenn to find Team Rocket.” mentioned Elm.

“Anyways, enough chitchat, let’s go get what you need for your Journey Jacob.” said Professor Elm.

They then walked over to a table in the room that Oak had been in that had some pokéballs, a PokéDex, a few potions, a Pokétch that looked different than normal ones, some running shoes and a backpack.

“These are for your journey Jacob,” Professor Oak said, “the Pokétch has been tampered with to be like PokéGear and is for video calls to and from us as well as others you may want to contact and normal Pokétch things.”

“And this,” started Professor Elm, “is a lead pipe,” pulling a gadget out of the Key Items pocket of the backpack, “just in case you get in a sticky situation, there are also many other gadgets in here for your journey.”

Jacob grabbed the pack and raked through it, seeing everything essential for his journey, and more.

“Whoa! So you’ve been waiting for someone starting their journey for a while.” Stated Jacob.

“Yes, we’ve been waiting a while for a new trainer to come here.” The two professors said in unison.

Jacob then grabbed the stuff on the table; put the Pokétch on his wrist, the loose stuff in the backpack, the running shoes on, his old ones in the garbage, and put the pack on his back.

When Jacob was on his way out, some terrible thing happened.

October 17th, 2009, 7:41 PM
Chapter 3
Team Rocket Returns

As soon as Jacob and Professors Elm and Oak entered the elevator and it started going up, they heard this terrible grinding sound, as if someone was drilling cement.

Through the glass of the elevator they saw a large digger drill with the red Team Rocket logo on it come through the wall and crush several agents.

An angry blue-haired man came out of the digger drill and started shouting through a megaphone.

“Surrender is probably the best choice you have at the moment, because if you do not, you will be killed,” he yelled.

Most of the people below put their hands up in surrender, but those who did not sent out their pokémon to attack the drill. While this was happening, Elm walked over to press the button that stopped the elevator so the three of them could watch.

The blue-haired man pushed a button that opened doors on the drill; about 9 dozen Team Rocket grunts with assault rifles appeared and shot the pokémon down to the ground.

The grunts then turned their guns on the attacking agents but some were able to take cover and brandish their government-issued firearms, immediately returning fire.

A few grunts noticed the people in elevator and fired on them. Luckily, the three of them were able to back out of harm’s way and the grunts ceased fire, thinking that they’d killed them. Elm hurriedly restarted the elevator.

As soon as they were at the top, they dashed outside and Elm ran into the house above the lab fearing for his wife and daughter while Jacob and Oak nervously waited outside.

While Elm was inside, the house shook and rumbled as if there were an earthquake. It felt as though the house might collapse. He dashed around gathering non-breakable belongings, throwing them out the door and over the stair railing. Other items like pictures in frames he grabbed and brought outside, his wife and daughter safely at his heels, arms full as well.

As Elm rejoined Jacob and the Professor, they realized the pokémon were still in the lab, and ran inside to gather the pokéballs. They each grabbed an armful. Oak got the last of them, and chucked the pokéballs out the door just as the house fell.

Not two seconds after the house fell, Professor Elm’s Pokétch started ringing, and Professor Birch’s face appeared on the screen.

Birch sounded stressed as he spoke. “We were just attacked by Team Rocket. Rowan didn’t make it; he was shot and killed by a grunt.”

Professor Elm answered, sounding just as stressed, “We were also attacked. My home fell just after we got the pokémon out. My wife and daughter are safe too, as well as a new trainer that arrived earlier this evening. Oak was not so lucky; he was inside when the house fell.”

Professor Birch sighed, “Well, I guess that’s good, but don’t you agree that it’s strange for them to finally reappear after all these years and attack both agencies?”

“It is pretty strange,” began Professor Elm, “that Team Rocket attacked us at the same time.”

Birch interrupted, asking Elm if he’d ever heard of a pokémon that was several shades of gray and looked evil, but Elm said he hadn’t and continued.

“How about meeting at Hoenn’s Elite 4 building?” asked Professor Elm.


The commander’s grunts shoved all the agents who had surrendered out of the Agency and locked them up in the drill. He called the grunts back into the drill, backed into the tunnel and blew up the agency.

After the lab fell, a few grunts made their way through a demolished wall and looked around, finding old Professor Oak alive, but unconscious.

They lugged the Professor into the drill and locked him up with the agents. The commander then drove straight through the shattered lab building and towards Hoenn, where they were to meet up with the others.

Commander Apollo, the man with the blue hair, the man that blew up the Whirl Islands just 20 years ago.

A few hours later the two Team Rocket groups met in the underground area of the Hoenn Victory Road.

“Commander Lance,” asked Apollo as they got out of the drills, “what is your report?”

“Well sir, we lost a few men, but eliminated all who did not surrender, including Professor Rowan; a grunt shot him after I yelled to cease fire, and I did execute that grunt. Sadly, Birch escaped.” explained Lance.

“This is news to me. Did anyone else escape with him?” asked Apollo.

“I think I saw a boy that looked to be in his teens, a trainer perhaps, but I’m not certain.” mentioned Lance.

“So you think you saw another person escape!?” questioned Apollo, “What about knowing how many you saw!? So how many escaped?”

“W-well, t-two, sir, I-I saw two, I’m certain.” mumbled Lance.

“If it was two, then of course it was a boy starting his journey or even just beginning a new one. A boy in his teens escaped with Elm in Johto, as well,” Apollo said snootily, “Oh yes, that reminds me… we captured Professor Oak alive, but unconscious. Grunts! Bring him out and wake him up!” he shouted.

A few grunts woke up Professor Oak and pushed him outside of the drill.

“What?” asked Professor Oak, “Where the heck am I?”

“You,” said Apollo, in answer to Oak’s question, “are in the underground of the Hoenn Victory Road.”

“Get your hands off me!” Professor Oak yelled at the grunts, startling them into releasing him, “I can walk by myself you know.” He pushed a button on his Pokétch, to send a signal to Professor Elm and then threw it at the ground, completely destroying it.

“Now, now, Professor, calm down,” said Apollo, “if you don’t cooperate, we will have to kill you. And we wouldn’t want that to happen would we?”