Takes place in the first past, when the Guardian is Pokémon no more, rather a force/presence made from Aura. It spans from the first landing of humans (back when Pokéballs didn't even exist) to hundreds of years into the future when Minami is once again threatened with the greed of humans. The Guardian and the One Tree are inexorably linked in this past.
The first part of the story has been in every draft ever since I started to write this story so long ago. It stands to reason then, the consequences of the boy Trainer's actions have changed as quickly as my mind does sometimes (the prose is also a lot better now in my humble opinion as well!). In the very first few drafts, Flareon and Lapras did exist, but their characters were written extremely badly. Not only did I not give both Pokémon a personality, the unnamed boy didn't really have one either...
The first couple of drafts didn't make sense. Things happened, but for no reason (without the cool stylistic way the Japanese make their movies), and there certainly was no inner motives from either human or 'mon. They just did things because I needed them to (I have by now learned this is one big pitfall made by heaps of amateur writers). The Guardian (who doesn't appear at this point any more) would not have made a tree branch fall on the Trainer, knocking him out, just because he touched Omneon. More realistically, Omneon would just get pissed, attacking by itself instead. Also, there is no more mini-ritual scene any more. It was weird and didn't make sense.
Although, I did end up keeping the turning-to-marble/crystal plot in the final write-up. In the final copy, however, when the boy touches Omneon, is suddenly privy to a deluge of strange memories, and, angered at this breach in privacy, Omneon goes to attack. But as he leaps, the light disappears and with it Omneon's power and vitality. It turns to crystal (something kept from the original you might note) and smashes into a million tiny pieces (a little more dramatic, ne?) Mostly because I saw the poetic justice of that particular curse, and that it was cool. :3 I was of course inspired with the children's book, No Flying In The House. If you happen to find this incredibly old but charming story, please give it a look. It's entertaining and if you happen to be one of those people who can find metaphor in everything, it will give you lots of ideas.
Trinyte - a.k.a Yin - was far more talkative and curious in the first couple of drafts. It only attacked when the human unexpectedly threw a Ball at it. Now, it attacks pretty much on sight, and gives the human fair reason to chuck the Ball in the hope it'll immobilise the legendary (although only Farell the Flareon knows of its legendary status). Also, originally, Trinyte's speech was so clichéd and horrible. You might also be interested to know that originally in draft one and two, Trinyte teleported them back to both Goldenrod and Saffron city, respectively. I eventually made up my mind by having him teleported back by the Guardian when it was still a Pokémon, and waking up in bed, which would set the way far more logically for the next part of his story when he told the press.
Before the rewrite, I fell into the trap of telling, not showing, the ramifications of the boy Trainer telling his story to the news. I explained it shortly in a paragraph or two, then went straight into the story of the next two people to actually make it to Minami. Having decided going straight to the story of those two people was a big mistake - I wanted to develop and extend the beginning of the story slightly - I had to go to either Kanto, Johto or Hoenn and introduce at least one more character. Thus, Dirk - and Kris - were conceived as characters to show us how people were acting with the news. Dirk's decision to take the plunge and search for Minami was pretty much assured from the beginning, however, the way it happened was totally unknown to me until I started writing and suddenly the two of them had personalities and motives. Well, Dirk anyway, maybe.