Summary

Everyone knew it would come eventually. Humans would find some way to gain power over the legendaries, control them, bend them to their will.

What they did not expect, however, was the mess that ensued.

Without the legendary Pokémon in the wild where they belonged, keeping things in order, the balances tipped.

Where they thought they had order, there was chaos.
Where they thought they had peace, there was war.
Where they thought they had achieved greatness, they had doomed themselves.

The wrong people took power over some of the legendaries, and epic battles erupted around the globe.
Entire regions were destroyed. The trainers who thought they had control over the legendaries perished.
The remaining legendaries lashed out at the human race for what they had done, furthering the mess they had created.

In a last-ditch effort to protect some of humanity, a large shelter was built underground. Only a small number of people were allowed in.
What was thought to be the saving grace for humanity wound up being a bloodbath as people fought for a place underground.

There was no bribing, no waiting. It was first come, first served. Even after the gates had been closed and sealed, the fighting above ground continued.
The legendaries continued to rampage, destroying everything that was built by humans.

This continued for several years. There would be occasional rumbling above ground, signaling that Pokémon were at work attempting to erase what reminded them of humanity. Very few Pokémon went underground; what few did saw what little good was left in the human race.

It has been five years since the last rumbling was heard. And a total of ten years has passed since the initial sealing of the gates. Most people have accepted and adapted to the way of life below ground. However, an ambitious few proposed that some try to explore above ground. Among those few was a Professor, ready to supply those willing to venture topside with a Pokémon of their choice.

There are many who are too afraid to leave the comfort of the underground, but there are rumors being spread around that some are prepping to head topside and examine the damages.

Who would be brave enough to travel topside?

The Effects

The ocean & the land.
With Kyogre and Lugia missing, the ocean has become still and almost lifeless; scarily so. Couple that together with the lack of anyone using it as a method of travel -- it's like a wasteland, only with water as the medium instead of land. With Groudon missing, the land has ceased to move and expand what was thought to be 'naturally.' Theoretically, this could be considered a good thing -- but when the land is unable to grow, the ocean, no matter how still, will eventually swallow it up. The water will chip away at the sides of cliffs, glaciers will melt and add to the amount of water, and ultimately, the water will come out on top. Though Kyogre and Groudon had their differences, they both had important roles in maintaining the balance of water and land. With Lugia gone and calm waters being the only thing, it would make things easier in theory, but, yet again -- it makes it to be treacherous for longer journeys, due to the hot sun hammering down on anyone caught out at sea.

Humans
Despite the thought that Pokémon are connected to nature, there are three Pokémon; Azelf, Uxie, and Mesprit; who are the embodiment of what are thought to be the three strongest things a human can have: knowledge, emotion, and willpower. With those three missing, emotion and willpower dwindled away by the masses. Knowledge became something that was not sought after, it was something that hardly anyone craved. There were those who persisted through the loss of these three Pokémon, and those were the ones who managed to survive somehow or another.

Pokémon
With the loss of Mew and Arceus, although it wasn't exactly known at the time, something was felt. Not just among the other legendaries, but among all Pokémon, wild and captured alike. Many younger ones became distraught, not knowing what the odd feeling was, and although one would think they would unify, Pokémon became hostile toward each other as well. Jumpy, paranoid, and agitated, some of the more aggressive species began to be avoided by Pokémon and human alike.

Life in general
With the Guardian of the Forest gone, and all other potential fill-ins captured as well, nature itself began to act out. Pollution quickly spread. Muk and Grimer became common everywhere, spreading the pollution further. With Xerneas gone, all life ceased to be created. Plant, Pokémon, and human alike; no new children were conceived, no new eggs 'found,' and no new plants were to be found.

Time and space
With the Guardians of Space & Time gone, space and time became irrelevant in some places. Some places were affected more than others. Time sped up in some places; in others, it slowed down considerably. And, even still, in others, it stopped altogether. The boundary between places was blurred as well; walking down a road could land you in the tropics, and turning around trying to go back could land you in the far northern reaches of the world. Known places are marked in some areas, but there are still a number of undiscovered blurs throughout Varosha that may be encountered.

History

There was once peace...

Varosha is but one place of many in the world. There were many people living together in Varosha in harmony. It was a good place to retire to. Despite its size, it was the most harmonious continent in the world. Food from around the world could be found in many places, Pokémon from all corners of the world were able to be found, whether as partners or in the wild. It had a very diverse climate, depending on where you went. A place for every Pokémon. Other continents and regions could not compare.

The leading place in peace and harmony, Varosha was the last to know about what was happening elsewhere.

Power hungry and determined...

In smaller continents and regions, petty fighting was common. Violence was high. Hardships were a part of everyone's life. A few desperate, albeit determined, few decided to rise up. Being highly intelligent, a select few banded together to attempt to create the ultimate weapon; The Gods Ball. It surpassed a Master Ball in the way that it would automatically capture any Pokémon, and it had no limit to how many Pokémon could be captured with it. It was highly advanced, with settings allowing you to choose which Pokémon you wanted to send out, all without the fuss of having to mess around with multiple balls. It bypassed the PC systems, so when used, one could potentially have dozens of Pokémon with them at a time.

To get to the point of The Gods Ball, they started off with not-as-great prototypes; capture rates being similar to that of Poké Balls, but still functioning as different levels of regular balls; the Poké Ball, Great Ball, and Ultra Ball. They simply named them 'Improved Poké Ball,' 'Improved Great Ball,' and 'Improved Ultra Ball.' They were a success and a huge hit. What they didn't advertise was the ball's abilities to house more than 6 Pokémon. Once this was discovered, however, the prices dropped and the the creators were in a pinch. They pushed forward faster than ever on the ultimate capturing device, and after a decade, were finally successful.

The first legendary Pokémon they tried it on was Kyogre. Without Kyogre in the depths of the seas, things began to change. Slowly at first, unnoticeable to those living on ground. But as more legendaries were sought out and captured by the trio, more change became noticeable. Other legendaries began noticing. They banded together after Kyogre, Groudon, Cresselia, the bird trio, and Entei and Raikou had been captured. That is when the war broke out.

The Pokémon, although they had previously been born with the unsaid inability to harm humans, tossed that idea out the window. Without the ancient Pokémon in their homes, things for Pokémon got bad. Although at first the idea was just to capture the legendaries to restore order among humans and help the world be a better place, it became a challenge, a game. Who could capture the most legendaries? The trio stopped caring about anyone but themselves and capturing all the legendaries.

Legendaries who had previously been hostile convened and decided they needed a plan of action, something to deter the trio from coming after them. At this point, the ones that remained wild were Mewtwo, Rayquaza, Victini, Reshiram, Yveltal, Giratina, and Suicune. All other legendaries had been captured by one of the three humans. It was decided that they needed to begin the destruction of humanity. There was much discussion about it; the debate lasted an entire week before it was set in stone. Each Pokémon was assigned a continent to take care of. Simultaneously, they began their assault. Mewtwo was assigned Varosha; he had a weak spot for humans, so it hurt him greatly to have to be so destructive to the most peaceful continent known to both human and Pokémon.

In Varosha, it was just another peaceful day. The destruction began on the west coast. The news was unable to spread due to Mewtwo being thorough in taking out all communications. However, as the days wore on and families were unable to reach loved ones further west, suspicions began arising. A dark cloud of dust and smoke slowly moved eastward. A few humans with trained Pokémon were able to escape and give warning. An emergency plan was put into effect; with the help of Pokémon who valued the lives of their trainers, a large underground shelter was built in three days. On the fourth day, the destruction reached the east. Many people who had heard of the potential sanctuary had flocked there. Those that had helped build it were the first ones in. A few Pokémon and their trainers were placed outside to try and keep order, but eventually they, too, retreated, to protect themselves from the violence outside.

Pokémon and human alike were fighting for a place in the shelter, as only a limited number could be allowed in. Out of the ten thousand or more that had flocked there, only a tenth were able to get in. The rest fought, and many lost their lives in doing so, and continued to do so, even after the gates had been closed and sealed with strong psychic energy. As Mewtwo reached the shelter days later, he pondered on whether he should force entry; he decided against. Fighting was still going on outside, with none taking notice of Mewtwo himself. He continued on, leaving the place and the fighting to take care of itself.

Not many survived...

A mere one thousand people were able to make it underground in Varosha. Only half were people who'd made it before the fighting. The other half had fought for a place. Many had severely injured, if not killed, other humans and Pokémon for a place. The latter half was confined to the outskirts, the place closest to the surface. The first half had the more luxurious interior, if it could be called that. They were divided, and called themselves 'The first half' and 'The second half.' The second half didn't respect those in the first half, but they got along due to the population being as low as it was. The first half was wary of the second half, scared that they would lash out and fight for a place on the interior, but luckily, that did not happen. Tensions were high for the first couple of years, but things smoothed out, and eventually, the two halves mingled with each other, and the bloodbath that had happened prior to the sealing of this place was all but forgot. The new way of life was accepted. Love was found, new families were made. Pokémon found love as well.

A hardy few survived above ground...

Unbeknownst to those who had retreated to the safety of the underground, there were a select few who survived aboveground. Those select few had gained the approval of Mewtwo himself and were allowed to live. However, once he left the area, the rest of the wild Pokémon were free to do as they wished. Many decided to try and ignore Mewtwo's approval and finish off these humans. Not many were successful, but the attacks kept on coming. The few that survived above ground became hardy, always expecting and ready for a battle at any level of threat, whether it be a few juvenile Pokémon, or a few strong, adult Pokémon. Most of these folk had been in the dark about the shelter in the east, so are unaware of it and are convinced they are the last ones alive.

Now...

Of the thousand or so people that now live in underground Varosha in the east, a couple were Professors. They helped take care of the Pokémon, and with the help of a couple of other enthusiasts who were eager to go topside, have convinced others that they should start exploring aboveground. However, for this, they need volunteers. And they aren't looking for young kids who are naive. They have set up a rigorous and somewhat annoying application process to determine whether or not they should allow someone aboveground. There are different reasons one can choose to go above ground, and depending on the reason specified by an individual, will determine what kind of Pokémon they receive, if the application process goes well.

The Professors themselves have not been above ground yet; they cannot leave the underground for extended periods of time, as they are looked to for keeping order and peace, and also perhaps the most knowledgeable humans in the underground. They are needed there.

The trio who had been capturing the legendaries is nowhere to be found. They seemed to have just disappeared. No one knows if they died, or if they are hiding in plain sight, or just hiding out in general. One would assume that things would be going back to normal quicker with them gone and the captured legendaries released, but there has been no word or sign from the trio or other legendaries, so it's safe to assume that they are hiding out somewhere, not wanting to reveal themselves, for fear of being thrown to the wolves for the near-extinction of humanity they had caused.

The other legendaries...

Were not too happy with Mewtwo's initial decision. However, despite their unhappiness, each one had found a select few to save in their respective continents as well, whether they wanted to admit it or not. Although Mewtwo's continent had the highest concentration of survivors, it was also the one that had the most destruction otherwise, and potentially the most violent wild Pokémon left. All of the legendaries retreated to the skies. They built homes there, to watch over their respective continents, with a psychic portal created by Mewtwo on each, to teleport each one to his domain should the need for a meeting arise. A neutral plateau was also created, but only accessible by Mewtwo's personal plateau. This is where the legendaries wait. They know that one day, humans will resurface, repopulate, and seek to potentially lash out at them for what they had done.