When Ghetsis was defeated atop N's castle most people had assumed N's dream had not only been doomed never to see the light of day, but abandoned by N himself. Team Plasma was a broken shell of its former self, its members in hiding or prison and it's sages having more or less accepted their failure. Team Plasma never recovered, and so the crisis was thought to have passed.
...However, what nobody had seen coming was that N's dream lived on not through N, nor Team Plasma, nor even Ghetsis, but through their admirers. A group of radicals operating low-key as scientists pursued to succeed where N had failed through their own, far less innocent methods. They sought to engineer something that could break the mysterious bond between man and pokemon under the guise of trying to understand it; and so they did.
First, they created a formula that could break the bond, and through further study they were able to initiate a kind of biological warfare unlike anything anyone had ever seen before. A virus was released which could infect and attack pokemon, removing their ability to develop or maintain bonds with their trainers or others in general.
The worst had yet to come however. From atop his celestial perch Arceus was not unaware of this act against... well... itself! From the dawn of the pokemon they had been meant to be companions to humans. Who dared commit such a crime? Arceus looked out and saw that the world had become uninhabitable for pokemon to live without losing their gift and was enraged. Just like that, he took back the gift of pokemon entirely. Pokemon rapidly began vanishing off te face of the earth, their spirits being recalled to a place not even the virus could reach them.
...And what of the humans? Humanity was alright, for a short time. There was great panic and with good cause however as humanity became intimately aware of how much it had depended on pokemon. Everything from the police, to rescue teams, to hospitals, to farmers, /everything/ had depended on pokemon to some degree. Without pokemon, some of these things were made impossible or obscenely difficult compared to before.
Crime ran rampant. Without pokemon there was no meat, and the produce supplies were quickly diminished. Humanity as a whole quickly devolved into chaos as people were forced against a rock and a hard place. In the end, humanity itself was nearly wiped put, though as the population declined it became easier for individuals to survive. Unspeakable horrors were committed in the name of life or death and a new era of depravity was formed. Children were the target of much hate, as well as those whom had them, humans beginning to looking at them as no more than extra mouthes to feed. Humanity eventually managed to stabilize itself, however. It was broken, but not down and out. Not even the scientists who had caused the catastrophe had been immune to the consequences, as they had no idea how dire said consequences would be.
It was not truly the apocalypse, however. Some of humanity stood strong to their morals even as demise was upon them. Though they were often crushed under the boot of the horde their stands did not go unseen. Arceus eventually found it in itself to seek a remedy to the situation, to spare a shred of mercy. Using its awesome power, Arceus restored the pokemon in a new form, that of which not even the virus could hope to corrupt. A quake of unimaginable power shook Mt. Coronet and tore it asunder. Yet, from the gaping wound in the earth erupted a giant crystal formation. The crystal shimmered with divine power and from it the spirits of the pokemon returned. From then on, children from the ages of 10 to 13 would feel drawn to the site, wherein the spirit of a pokemon would choose them and fuse with them, giving the child the ability to take on some of the features of that pokemon and access to that pokemon's powers.
In addition, a large stone tablet rose with the formation, upon which was carved the words "BRING YOURSELVES TO JUSTICE" in plain English as well as several commandments in a language that only pokemon spirits can read.
The commandments read as followed, and pokemon spirits are not only allowed but encouraged to tell their human host:
"The world has been broken, and it is humanity's fault."
"It is up to you to bring justice to yourselves and the world."
"You must guide yourself, however..."
"These are the laws of Arceus!"
•"Let yourself be washed of your moral preconceptions. From the first time you've read these commandments, let them be your only laws. Then and only then allow yourselves to rediscover what you believe is right or wrong."
•"You shall not harm the spirit of the pokemon, lest divine retribution strike."
•"You shall be in possession of no more than six pokemon spirits at any one time, lest your spirit become suppressed."
•"If you take the spirit of the pokemon from another you must take it for your own, lest it turn on you."
•"You shall not harm children under the age of fourteen that have not yet received their pokemon spirit."
It's now up to these children to change the world for better or worse. What will you fight for, and ultimately what will become of humanity and the world they live in?