
You start in a world and can go on any path you choose, there are gyms and a Pokémon league which can be a goal in and of itself, or just as a means to get stronger, but theres no single correct story.
There are factions in the world that you can chose to side with that shape the world and story.
Your choices and karma effected the world, for a random example, if you chose a path of a researcher you can get an end game with a mew quest, if you have a very moral, high karma run you can have an end game with a celebi quest, you could have an ending where you use technologies like shadow pokemon to rule with an iron fist, etc.