I just wanted to point out that, while the main characters in this story have the same name as the ones in my previous Pokémon stories, they are not the same characters. I suck at naming characters, which is why their names are the same. It's one of the reasons, anyway. Another is that they're named the way they are for a reason, and I'd like to hold on to that. The characters are not even related in any way. Consider this an entirely separate universe from the other stories', if you feel the need to.
Also, you may have noticed I don't go beyond gen IV. That's because I only know a handful of Pokémon from gens V and VI (mostly legendaries), as I haven't finished and started their games yet, respectively.
Another "also", this time related to this story. The first story block spoils who the villain for this story is. I wrote it before that occurred to me, but kept it because I thought it sounded cool. If you don't want to have that character spoiled, just use your browser's search feature (usually accessed by pressing Ctrl+F, among other key combinations) to scroll down to the first instance of "Blaziken".

There are many worlds in the Universe. They are each inhabited by different beings, but one kind of being is favorited amongst all the others: Pokémon. They were created by Arceus, the very first Pokémon in existence. After springing forth from a cosmic egg, it created four dimensions; one for Dialga, the Pokémon created to govern all of time, one for Palkia, the Pokémon created to govern all of space, one for several hundred – perhaps thousand – of other kinds of Pokémon, and another one for Giratina, whose destructive tendencies forced Arceus to imprison it in a world where it could do nothing but watch the other Pokémon while maintaining the balance between dimensions, lest they all collapse. The Pokémon lived in harmony with their respective worlds and with nature.
Then, something unexpected happen: humans appeared. They only existed in a tiny speck of a world in the Milky Way they named "Earth", yet Arceus believed they couldn't be trusted. They started off fairly peacefully: befriending Pokémon and asking for their help in some matters, which the Pokémon were glad to assist with. It wasn't long, though, before they invented devices to force Pokémon to live with them. Many Pokémon were glad to have a more permanent living arrangement, but the humans used the devices on wild Pokémon as well, who didn't want to be a part of their group – who distrusted all humans – and kept them around until their will broke. Some evil humans amassed armies of Pokémon to fight their wars for them. They didn't care about the Pokémon's safety. They just wanted power, and Pokémon were the way to get it.
Eventually, humans tried to create Pokémon of their own. They succeeded with a Pokémon they named "Porygon", but that wasn't enough. While the creation act was a great success, the Pokémon itself proved unreliable in combat. They quickly turned to cloning already-existing Pokémon. "Improved versions", as they called them. After hundreds of failures all over the globe, they created one out of the DNA of the ancestor of all Pokémon: Mew. And they named it Mewtwo. Mewtwo didn't know why it had been born or why it existed. It only knew it didn't belong anywhere, so it killed its creators and retreated to an island. It considered controlling the entire Earth with its powers, and even tried to do so with an army of clones, but it was stopped by a pure-hearted trainer. It then retreated, never to be seen again. After several years, Mewtwo discovered one of the improvements the humans had given it when they created it – or perhaps inherited from its DNA source, Mew – was agelessness. It didn't know that, though, until it saw its friends, the other clones, die from old age. Its heart grew heavy with sadness, regret, but, above all else, anger. Anger at the humans for having created it. Anger at the humans for not having told it about the full extent of its abilities. Anger at Arceus for having allowed this to happen. It wanted to die; to join its friends. However, it was too scared to take its own life. Instead, once it found a new power within itself, it fled Earth. It was difficult for the Pokémon to get out of Earth's atmosphere at first, but, eventually, it managed to focus its psychic powers enough to create a temporary barrier to keep itself from freezing. It drifted across space for what felt like an eternity, passing by a star every once in a while, in order to warm itself up. As it traveled, its anger grew larger, quickly turning to hate. It wanted to go back to Earth and make the humans pay for what they'd done. It wanted to take on Arceus. It wanted revenge.

"Humans... Arceus... You will feel my wrath. And this time... nothing will stop me."

On a planet in the Milky Way galaxy, a Blaziken was locked in a room. Ice-cold water was pouring from the ceiling above him, yet the Blaziken felt no cold or discomfort. He was standing under the endless stream, with his face toward the ground and his eyes closed. After a few seconds, a Blastoise and a Glalie appeared in front of him. The Blastoise hesitantly fired continuous jets of water at him, while the Glalie, also hesitantly, cooled them down. Their target still showed no discomfort, nor did he open his eyes, move, or make any sort of sound. He eventually froze, much to everyone's surprise.

"I-Is he dead?" the Blastoise asked.

Water kept falling from above for several minutes, yet there was no reaction from the Blaziken. The other Pokémon became increasingly concerned, until the Blaziken began to glow red, getting brighter with each passing moment. After the Blaziken reached a certain temperature, the ice quickly began to melt away. It disappeared completely, yet he didn't stop getting brighter and hotter. Eventually, the water falling on top of him evaporated before it even touched his skin. The air around him became distorted from the heat, and the entire room felt like it was boiling. The other Pokémon instinctively shot water at him, but all they could do was slow down the Blaziken's progress. The room got even hotter, to the point that the floor beneath the Blaziken burst into flames. Finally, the Blaziken opened its eyes and spat a single, continuous, wide line of fire at his attackers. The point where the attacks connected generated enormous amounts of steam, which quickly filled the room, making it nearly impossible to see. The fire slowly advanced toward its intended targets and heated up the room even further.
The Glalie was the first to succumb to the heat. He fell on the ground, yet his partner wouldn't give up. She redoubled her efforts, using both her cannons to triple her water output. The fire stopped moving forward, so the Blaziken pushed even harder. To conserve his strength, he stopped heating up the air around him to the point where the water crashing down only barely evaporated before touching him. This allowed for a greater burst of fire, giving him the advantage once again. His flames slowly pushed forward until they reached their target, who began to panic. She desperately tried to fight back, yet she couldn't. She tried to run away, but it was too late. Eventually, the fire evaporated the water she was producing before it even left her body. All that came out was steam. She finally collapsed with a loud thud, and the attack stopped.
The Blaziken finally took a few steps forward, in the direction of his attackers. He helped them back up while the never-ending water cooled the room back down and cleared away the steam. All three Pokémon were impressed by the Blaziken's victory. The Glalie and Blastoise complimented him, but he simply smiled and nodded while his eyes jumped from one Pokémon to the other as they spoke.
After a few minutes of nonstop compliments, a fourth party entered the room: a Lucario. The heat was just slightly bearable for him, yet he, like the Blaziken, showed no discomfort.

"Aw, man!" the Lucario yelled in disappointment. "Did I miss it?"
"Yes, Max." the Blaziken replied. "You missed it."
"Sorry, bro. I got up a little later than usual. Did you win?"
"He sure did!" the Glalie said happily. "It was amazing! First we froze him, but then he managed to melt the ice and did this thing with the air – even the ground was on fire! And then-"
"Calm down, Will... Excuse my friend. He gets a little too excited while fighting."
"Amber, is it?"
"Yup."
"Don't you get excited while fighting? I've never met anyone who didn't. It's in our nature."
"I try to keep emotion out of battles."
"That's... unusual."
"Emotion is weakness, Mr. Max. It makes you act recklessly."
"Emotion is strength." the Blaziken intervened. "It all depends on your control over your emotional state. If you learn to master your emotions, you master yourself. And then your full potential will be unlocked."
"I..."
"How do you think I won? You had the advantage. It was two against one. More than that; you froze me. I should've lost... but I didn't."
"What were you thinking about?" Amber asked.
"I was just..."

The Blaziken looked at the three Pokémon around him. He didn't want to share his feelings, as he only knew Max well enough to know he wouldn't try to take advantage of them. Will and Amber were a different story. He didn't know if they could be trusted. Although Amber had shared her story with him, he was still unsure if it was the truth or just something she made up.

"I... I'll tell you some day. When you're older."
"Aw, come on..." Will complained.

Amber knew exactly why the Blaziken wouldn't tell her or Will what he had focused on that allowed him to tap into his full potential. She was annoyed, but she tried to keep it to herself.

"It's fine, Will... If Mr. Blake doesn't want to tell us, it's his choice. Come on; let's go."

Will reluctantly went with his friend, who fought the urge to stomp out of the training building. As soon as they were out the door, Max turned to Blake.

"So... Just what were you thinking about?"
"You know what..."

Max stared at Blake for a while, looking for confirmation that what he thought was true. When he felt Blake had confirmed it with his complex expression, he sighed.

"...I understand, Blake."

To emphasize his understanding and calm Blake down, Max quickly wrapped his arms around his friend, patting his back just hard enough to be heard over the still-crashing water and reach Blake's ears. Blake hesitantly reciprocated the action, though he only patted his friend's back hard enough for him to feel it. After almost ten seconds, they released each other.

"I'm hungry." Max said. "You gotta be hungry too, after that fight. Wanna go get some lunch? I know how much you love pasta."
"S-Sure."
"Let me just turn off that water..."

Max hit a switch on the wall, and the doors where the water was coming from closed, stopping its flow.

"Let's go!"

Several hundred miles away, something crashed onto Blake's world. It fell from far beyond the atmosphere as a ball of fire, similarly to a meteor. As it passed the cloud cover, light burst from it, and it fell even faster. It finally hit the ground with enough force to create a shockwave that bent the trees by several feet, breaking several of them outright. The creature was injured and boiling hot from re-entry, but mostly starving. It slowly rose, trying to adjust to its new environment while also being held back by its wounds.

"This planet... The atmosphere is different... Thicker... Gravity's also stronger... It will take some time to adapt."

This creature didn't go unnoticed by a pair of Pokémon – a Medicham and his child – that happened to be passing by. They saw the fireball and heard the explosion, being startled by them. Meteor crashes were very rare, given their planet's twin moons and relatively clear solar system. Their thick atmosphere also meant that most meteors simply disintegrated before they even reached the ground. For something to actually hit the ground meant that it would have to have been enormous in size.

"Daddy, what was that?"
"I don't know, Jimmy... Stay here."
"Wait, daddy-!"

The Medicham left his child's side and rushed to the crash site. There, he found a strange creature struggling to breathe, covered in wounds, in the middle of a crater. He rushed to its side to help, but was immediately pushed backward.

"Come no closer, Pokémon."
"Poké-what? Look, I'm just trying to help. I'm Matt. Who are you?"
"Y-You can speak?"
"Of course! Why wouldn't I be able t-"
"These Pokémon... They're not like the ones on... Then he... Hm..."
"You're not making any sense. Just let me help you!"

Matt stepped forward again, yet the same strange force pushed him back even harder. Closing its eyes, Matt realized that the creature was the cause of this force. After this realization, he put more power into his legs and started moving forward very slowly.

"Stand back! I don't want to hurt you!"
"Stop this! I just want to-"

The creature finally jumped toward the Medicham and kicked him in the head.

"Don't think my wounds will make your life any easier, Pokémon... I will fight you to the death, if it must be."
"What in Arceus's name is a 'Pokémon'? And why do you want to fight? I only want to help you!"
"Arceus... You know of him? ...It doesn't matter. If you follow him, you are my sworn enemy."
"What? I don't-"
"Prepare to fight, Pokémon."
"Stop!"

The creature tossed a sphere of pure psychic energy at Matt, which only served to make him angry.

"If you want to fight... So be it."

Matt started running around the creature as quickly as he could, dodging every psychic blast it tossed his way.

"Stop moving!"

Without warning, Matt dashed toward the creature and struck it, coming out on behind it at the same distance he had been at when he was running around it. The creature dropped to one knee from the impact, making Matt think he had won.

"One punch and you're already on the ground?"
"You're stronger than the others..."
"What others?"
"It's no surprise... This planet is hard to get used to. It makes sense that you'd be stronger."
"What are you talking about?"
"You'll find out soon enough..."

The creature stretched its arm and painfully lifted Matt off the ground telekinetically, crushing his body.

"Foolish Pokémon... You cannot defeat me."
"Let me go!"
"No."

The creature tossed Matt around for a while, making him crash against the ground and even trees, before finally tossing him away from exhaustion. Both beings recovered for a few seconds, before going back to their battle.

Meanwhile, Jimmy had become worried for his father and was searching for him. Hearing the sounds of battle, he headed toward their origin and found his father battling a strange gray creature. It was unlike anything the small Meditite had ever seen in his life, though he was very young, so it didn't surprise him. What did surprise him was that his father didn't seem to recognize the creature either. Not only that, but his father was outright losing. He was running around it in random patterns, boasting about his strength and speed, but Jimmy could tell his legs were about to give out. Finally, having figured out the extent of his target's abilities, Matt decided to outsmart it instead of outrunning it. He stopped for a few seconds to gather his strength, making the creature think it had finally exhausted him.

"Are you tired already? I can keep going forever."
"I'm just surprised... I'm surprised you're so slow and pathetically weak."
"What?!"

Matt's opponent tossed an enormous ball of psychic energy at him, but Matt simply dodged one last time and turned invisible.

"I am well aware of your abilities, Pokémon. There is nothing you can do that can surprise me."

The creature closed its eyes and tried to sense where Matt was. It could feel psychic energy from all around it due to its own attacks, but one particular spot caught its attention, as it was the only spot where the energy was significantly stronger than average. In addition, the spot kept moving around.
The creature quickly deduced where Matt was and grabbed him telekinetically once again. Matt turned visible instantly as the creature slowly choked him.

"Let... me... go..."
"No."

Matt felt himself become lightheaded and closed his eyes. The creature thought it had won, as did Jimmy, but Matt surprised both of them by suddenly reopening his eyes, which were now glowing white, and pushed it backward with a scream. The creature instinctively released him and protected itself as it rolled backwards. Once it stopped, it stared at Matt in pure amazement.

"That's not possible... No Medicham has ever been able to do that!"
"Yeah, well... You're wrong."
"I must study you further... This battle is over."

The creature blinked, and its eyes turned purple. Matt took a few steps away from it, but it was useless. He felt his mind going blank, until his son's voice made itself heard in his head. He looked around, trying to locate his son. The creature, being inside Matt's head, heard it too and also began searching for his son. Jimmy sensed the creature inside his father's head and immediately cut the link between himself and his father, teleporting away just before the duo found his location. The grass where Jimmy had stood was waving lazily, in spite of there being no wind. Yet the young Pokémon had not abandoned his father. He simply moved behind the creature and tried to figure out what to do.

"I have to help my dad... I have to do something... I have to..."

Jimmy watched as the creature looked in several random directions and returned its focus to his father. Matt looked at his son in desperation, terrified of whatever was happening to him. Jimmy knew what he had to do. It was something he had never done in his life as, according to his father, he was simply too young. However, he knew he had no choice if he wanted to help.

"I have to get inside that... thing's head... Right now."

Jimmy closed his eyes and focused on the creature. It had strong mental barriers, but, thankfully, it was distracted with trying to control Jimmy's father. Jimmy was able to get past its psychic protection; a feat he immediately regretted having attempted. The flow of memories and emotions was overwhelming: first confusion, then anger, then pain, more anger, despair... It seemed that this creature had rarely, if ever, experienced any kind of positive emotion. Jimmy began to pity the creature, alerting it to his presence. It once again stopped what it was doing to Matt and searched for Jimmy, narrowly missing him as he finally teleported away from the forest.

"There was something there..." the creature thought. "I know there was."

"Do you know who or what was there?"

Matt slowly shook his head from side to side.

"Fine... You will obey me from now on, Pokémon. You will do as I command without question. If I tell you to kill, you will kill. If I tell you to destroy, you will destroy. If I tell you to acquire something for me, you will not fail. Do you understand?"
"I... I..."
"Do you understand?"

The creature's voice was all Matt could hear, especially inside his head. His own thoughts were drowned out by the angry, yet eerily soothing voice. His eyes rolled around, trying to focus on anything other than the creature, but everything else was blurry and cloudy beyond recognition.

"Answer me!"

Matt's eyes immediately jumped to the creature. It looked even angrier than before, completely blanking his mind. He blinked lazily, taking deep breaths, until he finally cracked.

"Y-Yes... Master."