The purpose of the mod is not only centric to the large Shivan/UIMS/Cylon/Battura/Bosconian/Sadeen modpack, introns and Shivan capship command... but also provide the future time many years after Capella, in a different universe where Terrans didn't develop space travel (see the 2018 film Mortal Engines). As of this writing it has no story, but I got an idea where it is set just after that film.
Okay. What you've described here is setting.
You want to tell a story about various factions (Shivans, etc) using two particular gameplay features (introns, Shivan capship command) in a setting after the Capellan supernova, without Terrans that have space travel.
I know you're very excited about Mortal Engines, but given that you've said it has nothing to do with your story both on the forums and in your outline, and that you've placed your setting into its far future, I'd suggest dropping all references to it as you're just making it more confusing. Part of telling a story and creating a setting is giving only the necessary details and leaving the rest to the viewers interpretation. There is a tendency among people new to writing to devote unnecessary writing and thought to setting and background at the expense of the things that are much more important, like story. Even certain experience writers do/did this.
Speaking a story I want to tell in five linear missions or fewer, perhaps one that revolves around the PVE pilot using Shattered Stars assets. While that has nothing to do with the overall Shattered Stars: A Deepness Within main storyline, it has ramifications that leads to the main storyline involving the Shivans.
In that campaign, set many hours after the last scene in the Mortal Engines film, the Vasudans are retreating from Sol after a series of defeats in trying to stop the UIMS invasion of Earth.
Or some non-Shattered Stars-related campaign?
Do I need to write a design document still? Since I need to write a story.
This is a bit of a mess, but lets break this down. You don't need to post answers to these questions (they'd fall under spoilers anyway), but these are the things you should be thinking about and developing before you even start building missions.
Storytelling means picking a theme - essentially, the lesson, thought, or meaning that you want to convey. Every story has a theme of some kind ( https://en.wikipedia.org/wiki/Theme_(narrative
) ) driving it, and storytellers convey that theme through the settings, events, characters, and plot of the story itself. So you need to decide what you want your mod to be "about." What message or meaning should the players get from playing your mod? You haven't identified anything that looks like a theme.
Next, what's the plot? Your plot takes place in an arc, with a beginning, a middle, a climax, and a resolution. You've described your beginning already: "the Vasudans are retreating from Sol after a series of defeats in trying to stop the UIMS invasion of Earth." In a video game, the "resolution" (denouement) is often a post-script, epilogue, or in the FSO engine, a final debriefing. That's something you write, rather than FRED. That means you have essentially five missions of gameplay (or fewer! more is NOT always better! some of the best stories ever written are SHORT!) to introduce your setting and characters, and create a beginning, middle, and climax of your story. Over a five mission campaign, that usually means 2 missions for introduction, 2 mission to develop the setup for the climax, and one for the climax itself. And just a note: having a climax and resolution does not mean you can't leave the story open-ended for followup. BP did this beautifully between AoA and WiH. You don't have to tie up every loose end - but you do need to provide some closure of the primary plot.
Finally, when you've got the rough sketch of the plot sorted out, you need to figure out how you want to tell that story. Who are the characters? What role does the player occupy? What level of agency (decision-making) does the player have in the missions themselves? How are the characters going to develop that story? What setpieces will be used?
It's only after you sketch out an outline of all of the above that you should even touch FRED.