It is very likely that this is going to be Magenta’s last major appearance in the story. She could still show up as a minor character later on.
P.S. This story was written in two hours after I had a dream about this.
Don't know where to begin?
While ultimately it doesn't matter which arc you begin with, Cecil arc is recommended if you want my recommendation.
And then Masu arc + Shattered union arc.
Feel free to visit the lore section as well which holds stories of its own.