A new story! It's not Advanceshipping, but I hope that you all will still like it! Enjoy! Disclaimer: I do not own Pokemon.

In a world where humans and Pokémon live together peacefully, a new evil threatens this long-standing harmony. The only way to stop this evil is for one human and his Pokémon to become one. This is the story of that one human.

Chapter 1: "How It All Began, Part 1"

"Aw, come on!"

Sixteen-year-old Seth Burns had a strained look on his face as he ran frantically after the school bus that was speeding several yards ahead of him.

"Wait up! Could ya stop, please?" Seth yelled as his short brown hair blew every which way in the wind.

Seth was currently wearing a navy jacket that he wore open, revealing his white t-shirt, a pair of blue jeans, and red sneakers. Hooked to the collar of his t-shirt was a pair of black sunglasses that he had not thought to put on.

As usual, Seth had woken up late and was now having to chase after the bus so that he could get to his high school, Hoenn High School on time. Believe it or not, however, Seth had actually set his alarm to the right time. There had been just one problem…

"Why did you electrocute my alarm clock?" Seth shouted angrily at his backpack.

Automatically, a small, pale yellow mouse-like creature with large, rhombus-shaped ears with black tips and additional black marks on its neck and tail, a short tail that was shaped a little bit like part of a lightning bolt, pink cheeks, and an extremely small nose that looked almost like a dot popped out of Seth's backpack.

"Pi-pi-pi-chu-pi-chu!" Pichu retorted.

"I don't care if the beeping was annoying you!" Seth spat. "It was to wake me up so that I didn't have to run after the bus! AGAIN!"

"Pi-chu-pi-chu-pi-pi," Pichu said, rolling his eyes as he held onto his sprinting trainer's shoulder.

"Oh, please. How do you know that she'll be able to…," Seth wasn't able to finish due to him suddenly crashing into the now stopped bus's opened door. He then fell backwards to the ground, along with Pichu, who was still holding onto his shoulder.

As he struggled to get back up onto his feet, he rubbed his now throbbing head until he heard a voice like crystal say, "Seth, are you all right?"

Seth's brown eyes widened as he looked up to see a girl about his age with blonde hair tied up into a ponytail and light gray eyes staring down at him. She was wearing a pink short-sleeved blouse and a short white skirt, plus a pair of brown sandals.

"Hey, Kelly," Seth said with a sheepish grin. "Guess you saved the day again, huh?"

Kelly Roberts smirked and rolled her eyes. She held out her hand and proceeded to helping Seth back up onto his feet. They then both got onto the bus and once again, the bus began to continue on its way to the school.

"I can't believe that you almost missed the bus...again," Kelly said as the two of them walked down the row towards the seat that she had saved for the two of them.

Seth just smiled as they sat down. She still looked pretty, even when she was annoyed with him.

He and Kelly had been best friends ever since the two of them were little. Through the years, he had developed something of a crush on her, but had yet to actually tell her.

Meanwhile, while Seth was deep within his thoughts, Pichu decided that now was the best time to crawl into the blonde teen's lap. As usual, she let him.

"Aww, you are just so sweet!" Kelly squealed as she hugged the Tiny Electric Mouse Pokémon. She then looked at Seth and said, "Why can't you be more like him?"

"You mean mischievous, destructive, and the destroyer of all alarm clocks?" Seth inquired sarcastically. "I think I'll pass."

Pichu looked at his trainer with an angry look on his face and sparks of yellow electricity dancing across his cheeks. Seth would've been scared if he wasn't used to his Pokémon's Electric attacks.

"Yeah, yeah, shock me all you want," Seth said to the small Electric-type. Pichu was about to do so when it changed its mind, deciding that it wasn't worth the effort.

Seth then looked at Kelly and asked, "So what's going on today?"

"Well, in case you've forgotten, which I'm sure you have, we have an battle test today in our 4th period Battle Class," Kelly answered knowledgably.

"Oh, great," Seth sighed. "What is it over this time?"

"We're doing single one-on-one battles," Kelly explained. "In order to pass, you have to beat somebody at least once."

"That sounds easy," Seth said, leaning back, shutting his eyes, and putting both hands behind his head.

"How can you say it's easy?" Kelly sputtered in disbelief. "There are a lot of tough trainers in our class, and this is the first time that winning was essential."

"Please," Seth yawned. "You and I both know that you'll win your battle with flying colors. As for me, I think I have a pretty good chance at winning a battle."

"Well, just don't take any risks today, okay?" Kelly cautioned.

"Come on, Kelly. Is it really like me to take risks?" Seth asked.

"Don't make me answer that question," Kelly crossed her arms and a teasing smile appeared on her face. Meanwhile, Pichu snickered at his trainer for his verbal defeat.

Seth groaned and said, "Why didn't I just get a Riolu for my first Pokémon like I wanted to?"

After a quick Thundershock, Seth was now on the floor of the bus and his body was black and smoking. Surprisingly, it had actually hurt a bit.

"Guess he can surprise me sometimes," Seth said, coughing up a puff of smoke while Kelly and Pichu simply laughed at him.

Later, during 4th Block Battle Class, Seth and Pichu smiled as the air was filled with the sounds that seemed to constantly emanate throughout the class. Explosions.

It was during this class that Seth and the rest of the Pokémon trainers—whether they were actual trainers, coordinators, breeders, watchers, future professors, future gym leaders, rangers, etc.—practiced their battle skills. In other words, it was one of Seth's favorite classes.

At this point, after having witnessed Kelly win her battle, Seth noticed another battle going on, and so he decided to go check it out with Kelly in tow.

On one side of the practice field was a short, bookish-looking kid with dark green hair and thick, wire-framed glasses over his emerald green eyes. He was wearing a collared, long-sleeved white shirt, a red tie, and a pair of khaki pants that were held up by a brown belt. He also had on a pair of dark brown dress shoes. The kid looked extremely nervous.

In contrast, on the other side of the field was a tall, bulky jock with cropped blonde hair and blue eyes, wearing a football (either football works, you choose) jersey, blue jeans, and a pair of green tennis shoes. He had an arrogant air and look about him.

"You're going down, kid!" The jock shouted over to the other kid, who began to tremble in fright.

Then, everyone turned to Coach Warren, who everyone had nicknamed "Coach Warzone." He was referring all of the battles in the class. What Seth didn't like about him was that he usually favored the jocks and preps over everyone else.

"Alright, this battle will be between our school's star athlete Nick Stevens," Coach said, gesturing over to the sneering jock. This caused a high amount of people to cheer. "And 'What's-His-Name' over there."

The kid that was actually known as Connor Wilson winced as he got several boos and hisses from the people on Nick's side of the field.

Connor was actually a year or two younger than the other sophomores, but he had skipped a few grades due to him being a genius when it came to the more book-oriented subjects.

"How can they all be such jerks?" Kelly muttered under her breath.

Seth didn't have an answer to her question, so they just continued to watch the battle.

"Okay, bring out your Pokémon!" They all heard the coach yell to the competitors.

"Machoke, time to strike!" Nick said as he threw a Pokéball into the air.

In a flash of blue light, a gray reptilian-looking humanoid creature appeared onto the field. Its body was practically made of muscles. It had red marks on its arms that looked stretched due to its huge muscles. It also wore a pair of black wrestling tights and a large, golden belt with a little red "P" on the buckle.

"Ma-choke!" The Superpower Pokémon roared while flexing its enormous muscles.

Connor's trembling increased at the sight of this muscle-bound reptile. However, he managed to pull out a Pokéball.

"P-P-Porygon, it's your turn!" He said timidly as he tossed the ball to the field.

Instantly, a virtual-looking creature with a pink polyhedral body and a blue stomach materialized onto the field. As it hovered slightly above the field, Seth noticed its blue triangular prism feet and a blue rectangular prism tail. It also had a pink polyhedral head that ended in a blue beak and had hexagon-shaped eyes.

"Machoke versus Porygon! Begin!" Coach yelled to the two trainers.

"Machoke, use your Karate Chop!" Nick blurted out.

Machoke jumped towards Porygon, aiming a glowing hand chop at the Virtual Pokémon.

"Porygon, use Conversion!" Connor instructed.

Porygon quickly used a transmitter to scan the oncoming Machoke. Its surface then glowed and took on a Machoke-like color pattern.

Machoke brought its hand down upon Porygon, who was able to hold against it for a few seconds before being sent flying backwards several feet. Porygon came to a stop after traveling about seven feet backwards.

"Machoke, hit 'em with a Fire Punch!" Nick shouted.

Machoke's hand became cloaked in red-yellow flames as it aimed a punch at Porygon.

"Porygon, use Conversion 2!" Connor ordered.

Porygon scanned Machoke's flaming hand and instantly its body took on a watery-blue color. Machoke's struck Porygon in the nose, but Porygon was only knocked back a few feet. It then turned back to its normal color.

"Okay, Machoke, it's time to use your Scary Face!" Nick sneered.

Machoke nodded and made a scary face that seemed to frighten both Porygon and its trainer.

"Now, use your Cross Chop attack!" Nick said, pointing at the pink geometric creature.

Machoke's forearms glowed white and it crossed its arms to form an "X" with them. It then jumped at the frightened Porygon and hit it with its crossed arms. Porygon was sent skidding across the field until it stopped a few yards away.

"Follow it up with a Vital Throw into the air!" Nick continued.

Machoke quickly ran towards its opponent, grabbed its tail, and then threw it up into the air.

"Porygon!" Connor cried out in fear.

"Take it out with DynamicPunch!" Nick said with an evil grin on his face.

Machoke clenched its fist and then jumped into the air after the Virtual Pokémon. Its fist took on a red glow and red-orange energy seemed to pulse off of it like an explosion. Soon, it punched Porygon and sent it hurtling down towards the ground, where it landed with a loud "THUD!"

Machoke landed back onto the ground as the crowd waited to see what happened.

As the dust cloud that resulted from the crash cleared, Porygon could be seen lying on the ground unconscious with swirls in its eyes.

"Porygon is unable to battle!" The coach declared. "Machoke is the winner! Nick once again wins the battle!"

Most of the crowd cheered for the star athlete and his powerful Machoke, while there were a few that felt pity on the sad-looking Connor, namely Seth and Kelly.

"Alright, Porygon. Return," Connor muttered sadly as he held out a Pokéball. The ball fired a red laser at Porygon that caused the Normal-type to disappear back into the device in a flash of red light.

What Connor didn't expect was to suddenly be lifted into the air by the elastic of his underwear by Nick's Machoke.

"You're so pathetic, nerd," Nick taunted him with a sneer. "You should've known that no one has ever defeated my Machoke in a battle."

As Connor began to cry, Nick and a lot of other people began to laugh at the poor boy's misfortune. Sadly, the coach wasn't doing anything about it. He was even chuckling himself!

Nick then looked up at Machoke and said, "Alright, let's see how far this kid can fly. Use your Vital Throw!"

Machoke grunted happily, and just as it was about to throw the kid into the air, a yellow blur came at it and struck it in the face with an iron-hard tail. Machoke stumbled back slightly, causing it to drop Connor to the ground.

"What the…," Nick began before he saw a brown-haired teen standing there, glaring at him. A blonde girl stood behind him and a yellow mouse-like Pokémon stood by his side, looking extremely angry at him.

"Hey, if you're gonna pick on someone, do it to somebody your own size," Seth shouted. "But just leave him alone!"

Immediately, Connor ran behind Seth and continued to cower in fright. This didn't stop Seth from glaring at Nick, however.

"This doesn't concern you, Burns!" Nick spat at him.

"I'd say it does," Seth retorted. "We don't like it when people pick on people that can't defend themselves, right, Pichu?"

"Pi-chu!" Pichu growled. Sparks of yellow electricity began to once again appear around his cheeks.

"Oh, so you think you stand a chance against me?" Nick sneered.

"Well, why don't we battle and find out?" Seth asked with smirk.

Just about everyone gathered around as Seth and Nick prepared to battle it out.

On one side, Nick grinned arrogantly with Machoke flexing by his side. On the other, Seth stood ready with Pichu standing on the ground beside him. Kelly and Connor both sat on a bench behind them.

"Do you seriously think that you can beat my Machoke with that little rat?" Nick called out with a laugh.

Seth smiled as he took a Pokéball from his belt and then enlarged it. "Who said that I was using Pichu?"

He then threw the sphere towards the field and yelled, "Gallade, take a stand!"

In a flash of light, a humanoid-looking creature appeared onto the field. It had a white lower body that consisted of bold rounded hips with strong legs. Its torso was thin and was colored in balance between the green of its upper body and the white of its lower body. Sharp red hornlike protrusions stuck out of its chest and back, and its arms were shaped like tonfas. Its head resembled a gladiator's helmet with its white face, red eyes, and light-teal colored head crest. In addition, there were spikes on the sides of its face.

"Ga-lade!" It said as it took a battle stance, extending one of its arms' elbows and making it look like a deadly blade. The crowd looked at it in awe.

"Begin the match!" The coach said to them.

"Machoke, let's show this poser a thing or two with your Brick Break attack!" Nick ordered.

Machoke's hand glowed white and it ran towards Gallade, aiming a karate chop at it as it ran.

"Gallade, use Teleport," Seth instructed.

As Machoke brought its arm down upon it, Gallade's body took on a multicolored glow and it also became surrounded in light blue vertical lines. It then disappeared, causing to stop and look at where the Blade Pokémon had been in shock.

What the Superpower Pokémon didn't realize was that Gallade had reappeared directly behind it.

"Machoke, look out behind you!" Nick bellowed.

"Gallade, use Signal Beam!" Seth commanded.

Machoke began to turn around, but as it did, the red horns on Gallade's body glowed light purple. A rainbow-colored ball formed in front of its front horn, and it then fired a rainbow-colored beam from the ball at Machoke, sending it flying several feet.

Machoke landed flat on its face after it landed, but it managed to get back up on its feet. It was now glaring at Gallade in what seemed to be a mixture of surprise and hatred.

"Machoke, get back at it with Revenge!" Nick shouted.

Machoke started to run towards Gallade in an angry rage, getting ready to uppercut it.

"Gallade, use Vacuum Wave!" Seth told the Psychic/Fighting-type.

Gallade jumped up into the air and its forearms began to glow white. It then spun around with its head and extended arm-blades facing its opponent and fired a horizontal tornado from its body at it.

Machoke was stopped clean in its tracks by the tornado and had to use all of its strength to avoid being blown away.

Nick growled and then yelled, "Machoke, take it out with Focus Punch!"

Machoke, in its maniac rage, ran at Gallade. Its fist glowed light blue as it prepared to punch.

"Gallade, finish it off with Psycho Cut!" Seth directed.

Both of Gallade's forearms began to glow light blue and they extended in the back. It then leaped towards Machoke, making a slashing motion as they passed one another.

As the two landed with their backs facing each other, only Machoke seemed to be panting while Gallade stayed calm. Suddenly, Machoke tensed up and then fell face-forward to the ground.

"Choke," It groaned as it laid on the ground with swirls in its eyes and a dazed expression on its face.

"Ma-Machoke is…unable to battle?" The coach said in disbelief.

Everyone stared at the unconscious Machoke laying on the ground in front of Nick in shock. Seconds later, they began to cheer loudly for Seth and his Gallade.

"But how?" Nick croaked as he gawked at Seth and Gallade. "Nobody's ever beaten me! Never!"

"Well, I believe I just did," Seth smiled. He then returned Gallade into its Pokéball and Pichu climbed up onto his shoulder before they began to walk off, followed closely by Kelly. The crowd at that point decided to follow the trainer while cheering frantically.

As they continued to walk amongst the applauding crowd who seemed to constantly try to ask him some questions, Seth noticed a guy who was leaning against the wall a good distance away staring at him.

He had short, black hair that he kept under a black fedora and cold-looking brown eyes. He wore a pair of khaki cargo sorts with a wallet on a chain attached to them, black tennis shoes, and a t-shirt that had a picture of a skull with a number 7 in its forehead on it. Around his neck was a class ring with an aquamarine gem in it with a silver thread going through the ring. Seth figured that he was probably a couple of inches taller than him and looked both strong and menacing.

As both of their eyes met, Seth felt a strange and ominous tension in the air between them, almost like they were born to fight one another.

"Hey, Seth!" The tension broke as Seth heard Kelly call his name. He looked to her as she said, "Let's hurry and get to lunch!"

Seth shook his head and gazed over at the wall again, but the guy who had been there was gone.

"Yeah," Seth said, scratching the back of his head in confusion. "Let's go."

As the school bell rang, everyone walked out of Hoenn High School happily, including Seth, Pichu, and Kelly, who were once again walking home together. Although they took the bus in the morning, they liked to walk home in order to talk for a while about the day's events.

However, they had only gone a few feet past the school gate when they suddenly heard a voice call out, "Hey, Seth! Wait up!"

Seth and Kelly turned around, and were surprised to see a panting Connor run up to them.

"I just wanted to say thanks for saving me from Nick earlier today," Connor said, looking up at the brown-haired teen with a smile.

"No problem," Seth replied with a smile. "It was my pleasure."

"Pi-chu!" Pichu nodded from his trainer's shoulder, happily grinning.

"Hey, Connor," Kelly began. "Did you ever win your battle?"

Connor nodded sadly, "Yeah, some guy felt sorry for me and let me win. I just wish that I could win my own battles for once without any help!"

Connor lowered his head and began to sniffle as tears built up in his eyes, but he stopped when Seth knelt down in front of him.

"Well, that's never going to happen, because you can't win any battle without your Pokémon," Seth said with a serious look on his face. "In order to be a truly great battler, you need to be at one with your Pokémon. You must have one mind with one goal. Only when you are fully in sync with your Pokémon can you bring out your true potential."

Connor and Kelly stared at the trainer in awe. Connor then wiped the tears out of his eyes and said, "You're right. Thank you. I won't stop until I'm one with my Pokémon."

Seth nodded and stood back up with a smile on his face. He and Kelly then waved while the green-haired boy happily ran off with glee.

Seth continued to stand there and watch the boy run off proudly until his train of thought was broken when he heard Kelly say, "You know, that was pretty deep. I never would've expected something like that from you."

"Well, actually, I didn't come up with that myself," Seth admitted. "That was something my dad used to tell me all of the time when I was younger, before he…disappeared."

Kelly looked at her best friend sadly. About five years ago, Seth's dad had disappeared after several failed experiments at the lab where he worked. Since then, Seth had had to grow up on his own.

It was actually quite sad. All Kelly wanted to do was embrace him and hold him until he felt alright, but if she did, then her true feelings for him would be revealed.

For years now, Kelly had developed strong feelings for her best friend, but she was afraid that if she told him, he might not feel the same way and their friendship could possibly end. Their friendship was way more important to her than any feelings of affection.

At that, the three of them proceeded to continue making their way towards their homes.

Meanwhile, in an office many miles away, a man sat in a chair behind a particularly large desk, surrounded by shadows so that no one could see his face.

At the side of the chair was a large, green dinosaur-like creature with an armor-like hide, spikes protruding from the back of its head, neck, shoulders, and the tip of its tail, and several holes at the knees, its back, and four on its chest. Also, there were two blue rhombus-shaped pieces of armor that covered the creature's belly and back, and to add to its menacing appearance, it had fangs in its upper and lower jaws and its fingers and toes were culminating in claws.

Suddenly, a female voice was heard over an intercom saying, "Sir, the three agents that you requested are here."

The man then pushed a button on his chair and said, "Good, send them in."

The door of the office slid open and three figures walked in. The man could not discern their features in the darkness, but he could tell that one was female and the other two were male.

"Sir," The three of them said in unison as they knelt before him.

"Agents Headsmasher, Primrose, and Iceclaw, I have a mission for you," The man stated as he pushed another button. Suddenly, a hologram appeared on his desk. "This device is the target. I have already sent Agent Camouflage after it, and you are to pick it up from him and bring it back to me. Understand?"

"Sir," The three agents nodded. They then stood up and began to walk out of the office.

After they left, the man in the chair chuckled and muttered, "Soon the power that I crave will be mine. The power of perfect fusion."

Next Chapter: Chapter Two: "How It All Began, Part 2"

So, was it good? Bad? Tell me what you think! Read and Review! And no flames, please!