You meet a Ninetales at a shrine who solemnly predicts that you will be a great Master someday.
You pass the shrine repeatedly and you can pay them respects each time, receiving wisdom. You can also flirt with the 600 year old fox, who is amused but slowly begins to flirt back. They share many stories of their experiences, and eventually begin to care for you. You receive mail with helpful wisdom and items from the Ninetales.
Eventually, you return to the city, warning that a cataclysm is coming. Nobody believes you.
When the cataclysm arrives, you are separated from your Pokemon. Two options are possible. Stealth mission to get back to them, or, if you romance the Ninetales hard...
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The Ninetales bursts from the wreckage of its shrine and joins as a temporary party member. It has maximum level and stats and literally blasts its way through opposition to reunite you with your Pokemon.
It then collapses, having spent a year of its life for every minute of super power that it had left, and you have to carry it out of the city, where it joins your party. It isn't very powerful and complains occasionally of aging. You can keep romancing the Ninetales, who eventually comes to share its tails with you at night.
Before the BBEG, you are given an option whereupon the Ninetales offers to engage super power mode if you ask and your romance level is high enough. If you choose and defeat the enemy, the exhausted Ninetales reveals that it has approximately 74 years of life left, or about the span of one mortal lifetime... but it's fine, because after you go, they won't want to live anymore anyway.
The Ninetales nuzzles your hair. *Shh,* the ethereal voice whispers. *Don't cry. You are worth it.* A lick-kiss to your cheek. *You have always been worth it...*