OK, I will spoil the story for you:
The main character (you), wake up in the forest, with no memory of the past, except that you know you were human before.
Another Pokemon (your partner Pokemon) helps you up, asks your name, and make fun of it.
Suddenly, a mother Butterfree comes rushing to you and ask you to help her baby Caterpie.
Your partner goes on and explains that recently, "untamed, uncivilized" Pokemon are getting more and more aggressive, due to frequent natural disasters.
After saving the Caterpie, your partner suggests opening a Rescue Team.
The next day, a Rescue Team starter kit arrives at the post, and you guys start you new Team...
That night, the main character sees a mysterious dream (as the game goes on, the dream becomes more clear, and you findout the shadow is a Gardevoir - yes, this dream is reoccurs a lot).
[Your rescue team handles many jobs, such as Rescuing the Diglet child, finding the lone Magnemite etc]
Soon after handling many jobs, your Team gets more famous, but the fact that you are an ex-human catches Gengar's attention.
He spreads the story that your existance is the cause of the frequent natural disasters, because it is the same with "The legend of Ninetale's curse".
[The legend of Ninetale's curse: a careless trainer pulls one of Ninetale's tails, and nearly gets cursed. However, his fateful Gardevoir gets cursed instead, and dies. Ninetales asks the trainer if he feels bad for Gardevoir or not.
Instead of answering, the trainer runs away. This leaves Ninetales in sorrow, and in her anger, curses the trainer so in his next life, he will become "a lowly Pokemon"]
A mission to other Rescue Teams are issued.
To kill you, so the natural disasters will finally come to a halt.
With your partner, you run away, trying to evade attacks by other Teams. Along the way, you tagup with Absol, who senses you are not the cause of the disasters.
After reaching a mountain, you fight with Alakazam (a famous and powerful Team leader). However, the fighting is stopped by Ninetales. You ask if Ninetales cursed you...
But the answer is "no". You were not the human Ninetales cursed.
After regaining your status as a "Pokemon", you and your partner return to town.
[Here, you go through more jobs]
You hear that Blastoise has not returned after exploring a certain cave, and you and your partner decide to explore. However, Blastoise returns, and warns that the earthquakes are caused by the "fire God" - Groudon, and Blastoise tried to stop it but got defeated.
[You and your partner go to the cave, and defeat Groudon]
However, even defeating Groudon did not stop the earthquake (along with other natural disasters).
Suddenly, Xatu warns of a meteor heading towards the Earth, and says that only Rayquaza can stop it.
You and your partner fly to the Sky Piller (aided by "flight crystals" created by the power of Xatu and Alakazam... and although revealed later, Gengar), and try to ask Rayquaza for help. However, it attacks you, thinking you are the ones causing the disatser, and you are here to get rid of Rayquaza.
After solving the muddle up with Rayquaza, it helps you... and fires it Hyper Beam towards the metor, destorying it, but also blowing you and your partner off the Sky Piller.
Saving the Earth, everyone feels proud for you, and congraduate you.
But you notice you are starting to dissapear... your partner tries to stop you from disappearing, but it is no use, and you spirit gets knocked off to space "where you belong".
Your partner cries, calling you a lier "because I wanted to continue the Team with you! Without you... without you... lier... lier...".
In space, someone asks you a quesion "would you live with them, or return to your human self?"
No one can hear what you say.
As your partner cries in front of the Team HQ, you return to Earth.
Everyone is brightened up, especially your partner.
[Ending]
(btw, the you might be wondering who the human cursed by Ninetales really was.
Actually, it is Gengar).