When writing a plot for a fangame (or anything really), I try to keep my thoughts organized in tiers of detail and granularity.
(Keep in mind: this is just a process that works for me. There is no "right way" to create!)
On the top level, the
Macro Tier, I include things like: story themes, general motifs, and major characters. Many of the best stories have a hidden theme that ties them all together. Most official Pokemon games have the central theme of a
coming-of-age story, where the main character & friends grow over time, through hard work and overcoming adversity. With your Fan Game, you may want to borrow that theme if you are going for a classic Pokemon game feel, or maybe you want to do something different, like writing a more mature protagonist, or a smaller-scale story. But the theme helps you conceptualize the entire game on a broad scale: where is your main character at the start, versus the end of their story? What is standing in the way of them achieving their goals? Keeping this in mind will keep your narrative tied together nicely.
Also in the Macro tier are
motifs. Motifs are like the symbol that makes your story unique; it should probably be in the title of your game. For example, in
Pokemon Gaia, the major motif is the Earth and what lies below. In my game Pokemon Uranium, the central motif was Nuclear radiation, which defined both the main conflict in the story as well as the color scheme. Your motif could be anything, from
Time Travel to
Glitched Corruption or anything really. Try to incorporate your motif as much as you can, and the story will be stronger for it
Finally, in the macro tier I put a list of the major
characters in the game. In standard Pokemon terms this includes the player character, their rival(s), mentor(s), family members, main antagonists, Gym leaders, etc. I would put careful thought into these characters, because again, they are a big part of what makes your game memorable. Give each one a unique name. If you like, try giving each character a motif of their own, such as a particular Pokemon type they like to use.
Next is the
Middle Tier. This includes stuff like: The backstory leading up to your game, the Region design and layout, lore, etc. You don't need to go too in-depth with this stuff, but having a rough framework of locations, like "A peaceful town surrounded by flowers" or "A dense network of underground tunnels dug by Pokemon" will give you a general sense of what to put in your game. Again, don't spend too much time on this, but do think a little about how your region's map will be structured, where different types of Pokemon will be located, as well as any new game mechanics you want to include, and how you will incorporate them.
Finally, the
Micro Tier, is ironically where you will be spending the majority of your time writing. This tier contains the actual dialogues and content that goes into the game, such as trainers' teams, item locations, puzzles, etc. When writing story dialogues, I do actually write it out like a movie script, with "stage directions" for events that take place around the dialogue tags. Of course, this step is optional, as you can simply put these in RMXP, but I find it does help to write them out in a document first before inserting them. That way, you can read it over with spell check and catch typos and awkward phrasing before it goes into the game.
One final tip. When writing dialogue, keep it short and sweet. The in-game text box is small, so short sentences are better than long ones. Players will also pay better attention if you use fewer words but keep them impactful.