I tried to think of a good story for the game, and here it is. (I may change the entire region or just add new towns/cities)
You start in a strange dimension, and you see Team Sun/Moon trying to capture a legendary Pokemon. You don't know what it is, and when you try to help the Pokemon, you wake up. You try to explain your dream to your parents, but they won't believe you, so you decide to go to Professor Maple's Lab for a Pokemon. When you get there, you find your two friends also getting Pokemon. They say they dreamt about a legendary Pokemon, and no one believed them, so they are going on a journey to try to prove that they saw it.
As you go further through the game, you learn that Team Sun/Moon is an evil organization that captures legendary Pokemon and hurts trainers Pokemon.
Once you get to Timeflower City, a city known for its Psychic trainers, a psychic tells you that you have the ability to see the future. However, when your friends arrive, one of them can heal Pokemon, and the other friend can talk with Pokemon. Using this, you can look into the future to see who needs help, then one of your friends talks to the Pokemon to see whats wrong, and the other friend heals it.
At the top of Mt. Relic, you find the legendary Pokemon from your dream, and you hear helicopters approaching with Sun/Moon grunts. You are in the same area you were at in your dream, and your friends are not around, so you have to save the Pokemon yourself, and if you defeat all the grunts, the boss will battle you. After defeating the boss of the team, the legendary Pokemon trusts you and joins your party, but if your party is full, the Pokemon makes you deposit one into the PC.
Bonus Missions: Lost Pokemon Hurt Pokemon
Azurill Wynaut
Skitty Whismur
Riolu Budew
Shinx Togepi
Igglybuff Ditto
Dratini Caterpie
If you like the story, I'll change the one on the first page.

Here is what the first town will look like (Without a new tileset)
If you look at the house in the bottom left, you'll see something blocking the way to the door. I fixed that.
__________________
Find me on Discord or whatever. @Wobb#2777