God... your plot is something completely bizarre and nonsensical. Honestly, it feels like an exaggeration parody on bad animes. The connection with the gameplay world is minimal, with absolutely no impact, and the whole plot is just several isles of events in a void of plot holes. There's no continuity with handwaives to past events or predictable or simply rational outcomes. Characters are just some anime/manga stereotype Marry Sue - level badasses with no fleshed out personalities or understandable motivations, almost all of the plot can be removed without impacting the game story.
Really, I recommend you to either cut down the presence of story on the map to minimal, that is, almost zero, with no details, or completely, like, absolutely rework the story after learning more about proper story development - at the current state the story is just gibberish that will confuse anyone willing to read it.