I intended from the beginning for nature to be a chaotic, endless struggle of living things against one another for both greatness and survival. This ethos of struggle is echoed today not only in the wild, but also in pokemon battles; early Man understood this, and for this reason described the changes of an individual from aging, growing stronger, or other methods with the same term for the changing of species over time.
Just as the struggle of land and water become unbalanced, so can that between species. I created Zygarde, like Rayquaza, as a god of balance who would replenish the world's ecosystem whenever the battle between Yveltal or Xerneas – between overpopulation and extinction, between life and death – skewed too far in one direction.
Yet there is no denying, in this world of rapidly growing human population and settlement, that this balance has leaned too far in Man's favor, prompting many to ask where Zygarde has gone. Some have suggested that humanity, being made in the gods' image, was immune to Zygarde's wrath – others have suggested Zygarde sees its role as an arbiter between civilizations, or that it opposes only the destruction of nature created by cruelty or indifference, not by ordinary settlement.
Neither is true. In reality, Zygarde has not intervened in human affairs because, although a god, it remains like all of us a pokemon – and Xerneas, in an ingenious loophole, has ensured that it will always have a trainer. This trainer was long an immortal king named AZ, short for Arceus-Zygarde (a religiously-inspired regnal name,) and he is on the side of Xerneas. Rumors of his soul finally passing after the Team Flare incident would not upset this balance, for Zygarde has since been reported in the possession of a great hero from Vaniville Town.
This concludes Pokedex for the time being. Diancie's movie has been announced, so I'm waiting on it to write its entry - Hoopa and Volcanion I plan on writing around the time of their events, unless we know enough about them by then that I can write them after Diancie. Thanks to everyone who's helped me with ideas, read over my stuff, or just encouraged me with comments - it's been a wonderful journey.