Once upon a time, there was a princess, daughter to the king's younger brother, whose one request for her birthday was a pokemon all her own. The younger brother sought far and wide for a pokemon to please her, but each she refused, saying 'But there are others like it! I want one only for me!'.
A year into the search, a scientist under the employment of the royal family came forth with an idea: what if they could make the princess a pokemon? So started experimentation with the idea of artificial pokemon, and created the Soul Heart. But on its own, it was just a container; an empty shell. So the Legend of Life, Xerneas, was sought out.
It took extraordinary effort, but eventually it was found. The Soul Heart took in Xerneas's Fairy Aura and whirred to life, but that alone was not enough. Every time the scientist placed the Soul Heart in its body, it twitched and jerked, then ejected itself. It rejected the body, but why? Was it not alive? Or... not complete. Xerneas was only part of a greater whole, so perhaps the Soul Heart needed more. So, the scientist sought for Xerneas's other half, the Legend of Death, Yveltal. It took even more effort, resources and time than it had to find Xerneas, but the scientist succeeded once more. And in Yveltal's presence, the Soul Heart drank in its Dark Aura.
At long last, the Soul Heart was complete. When given its body, the Soul Heart accepted it. Embraced it, even. The scientist was overcome with emotion as the artificial pokemon stirred to life, opening its glowing eyes and taking its first steps. Then, the pokemon was given decorations, colors of red and gold, so to be a thing pretty enough for the princess. Upon being presented, and the princess assured that, yes, there is only one, the princess announced she loved it, and dubbed it 'Magearna'.
It was many years later that the war broke out, and the king's floette was sent off, and what returned was a little box. The king was distraught, and set about seeking a way to return his previous friend to life. He turned again to the scientist. If an artificial pokemon could be made from nothing, surely another could be brought back to life.
So the scientist set to work once more. At first the scientist thought build a new body, and have the floette's soul reside there, but it was impossible to tell where her soul might be. So instead, it was decided to pull the soul back to the original body. But again, there were problems. How could a machine connect body and soul? It would need to harness the power of Life and Death!
An epiphany. There was a pokemon in existence like that. But the princess doted on the pokemon, and would not likely part with it. The scientist brought the idea to the king, who latched onto it with frightening intensity. He was the king. If Magearna was needed, it would be pried away by force if necessary. The princess begged and pleaded, don't take it away please!
The king ignored his niece. Taking the pokemon, he ripped it away from the girl, bringing it back to its creator. The scientist's heart broke upon seeing how confused, despondent and distraught Magearna was from being away from its only friend, but said nothing, and continued the work. When the time came to put the Soul Heart in, the scientist wept tears of sorrow, both for themselves and Magearna, as the pokemon could not. It did not deserve such a fate. Through their tears, the scientist took the Soul Heart from its body, and stored the body away within the machine. Magearna would not be without both its parts.
The king's pokemon was revived, but saw that he was no longer the same man she knew. So the floette left, leaving the king in further despair. In his anguish, the king demanded the machine be turned into a weapon. The scientist was to comply, or die. So they worked.
As the scientist placed the Soul Heart within the Ultimate Weapon, they murmured a prayer for the artificial pokemon, to anyone that would listen 'Magearna deserves to live, and grow and learn. Please, let it be released and allowed to be free, free to be as it pleases.'
The wish was heard, but it would not be for 3,000 years that it would be fulfilled.