PART 1: OVERALL PLOT
every game needs a plot, and preferably a good one * cough * fates. And, in my roughly 3 years in the larger fire emblem fangame community, (and in my 7 plus years of writing and reading) hackers tend to write quite disorganized,( because making a plot is difficult.) consider writing in this way and see if it makes it easier.
What you’ll need to do first is make a rough outline. What I like to do is find three-five big points of interest
<roy is forced to take control of the lycian league and liberates ostia
<roy is commanded to go to the western isles by etruria and frees the isles
<roy marches on etruria to save them from bern
<roy pursues roartz and alucard to either sacae or ilia and learns about Idunn
<roy marches on bern to defeat zephiel and Idunn
now, fe6 isn’t what you’d call “a particularly unique experience” but it is good on learning how to write due to its simple story.
TLDR: make a outline with all the major plot points of your story and fill in the space between the points
PS another thing to mention, it’s OK if these plot points change over the course of your game, stories evolve as you write them.