Story Help?

Okay so I have this idea for a story:

There's this island with a high-class trainer school on it. Every year the graduating trainers have to travel the island beginning autumn, which is almost entirely deserted this time of year. To pass they get a list of about 10 different challenges to do along the island. Some are gym-like challenges others are to capture a certain Pokemon or a certain amount.
My story will be following 2 very different girls that are both trying to complete their challenges in the allotted 9 months.

The only thing I still need is a conflict, or something besides the exam they need to solve.
I don't want anything with teams, I think everyone has seen enough of team rocket or whatever demented team is trying to take over the world.
I was thinking maybe a legendary Pokemon that has gone berserk in any way, or something along those lines.
Does anyone have an opinion or an idea?

Thank you beforehand =)

Hmmmm perhaps a hard to catch pokemon?

Or rather, the island school thing could be a sub plot, wherein, something like the legendary pokemon that interferes could be the main portion.

Perhaps it is an intensifying rivalry between your two characters?

Conflict with one's self?

But yeah, with so many legendaries, you have a lot to choose from.

Heres an example I just thought of:

You're on the island, but the island still has a previous occupant, Mewtwo. Because this is the school's first year, it seemed okay at first, but then, your character's and others, will begin to catch the cloned pokemon, which Mewtwo will not appreciate.

It would definately make for an interesting plot, especially if the majority of the rich folk come from a spoiled background.

I prefer not to bring in Anime things, like Mewtwo and its colony of cloned Pokemon, but thanks anyway.]

The thing is, I want the two characters to not know each other until they meet about halfway through the plot.

I was thinking, perhaps that the Pokemon will be behaving strangely because one of the Legendaries (One to be linked to the Island) will be restless.

I might be able to make one up, but I only want to do that when everything else fails.

Yeah, I can see that definitely working :)

If the two characters have not met up before too, it leaves you to their mercy, in that you could create some really funky personalities that would make for great clashing moments XD

I got it!
Palkia goes Primal as the conflict!
Huh? HUH?

Okay, I have decided to initially make it about the Weather Trio. I will probably also associate both girls with Groudon and Kyogre, they will meet them on different occasions.

There will also be another character associated with Raquaza, someone that will be familiar with both of the other characters, but will be travelling with one of them.

Now, the next question is, what will be the cause of the two Pokemon's restlessness?

heh XD Pollution? (though it doesn't seem prevelant in the pokeverse anyway).

Perhaps it can be a result of unrest from another legendary trio (like the birds).

Perhaps some one was seeking out to destroy them?

And to go off a bit more of a whim: Perhaps the two connections the characters have should not have had them met, so that the unrest is because of them though they don't know how or why, or what of it yet. (I randomly thought of that when I remembered that cartoon about those extinct dragons in a ice/fire land, where two tribes have been fighting over each other forever. The son and daughter of each respective tribe likes each other, and when they were young, were "gifted" with dragon abilities each of fire and ice... Bad summary is bad Oo

Haha I can totally see them going berserk over pollution xD

What do you mean it's about them. Could you please elaborate on that, it wasn't really clear..

Actually, come to think of it, the pollution might not be so bad. As long as it's not all cliche, OMG, everyone's killing the earth, I just teach them a lesson! Like the anime usually is xD

seeking to destroy the weather trio rather, though if I recall that sort of occurs in the anime, or rather to harness their power, I think... idk, lol.

Perhaps because the pokeverse seems so environmently concious, it could be a Team that goes all out and starts polluting?