THE ORDER OF WRITING A NON-LINEAR NARRATIVE

I think the way you're writing the main story is the problematic part, more than the way you're writing the sidequests. Planning is good. The more knowledge you have of your characters and your story direction as you're writing, the better. I don't always follow my own advice, but as a result I almost always have to go back and edit everything I wrote earlier in the story to match the stuff I came up with later.

With that in mind I think you should be able to do just fine writing the optional stuff after you're done the main plot. You now know exactly how much the characters know about each-other at that point in the storyline and exactly how much they'll know about each-other by the end of the game, and you can write the dialogue in such a way that it makes sense and feels meaningful for both of those situations and for any other point in between. I wouldn't do it any other way.

Make a flowchart of the game. What kind of nonlinear game will it be?

Static Non Linear: A game with a few deviations in the main plot like doing 2a instead of 2b, and leading the player to have a few endings. Flowchart Layout: Like a string with a few different threads spreading out.
OR
Dynamic Non Linear: A game with many choices that can dramatically affect the story.
Flowchart Layout:Like a web


Here are some handlers on designing major story elements if a main quest required the completion of a side quest:

• Prevent story progression until the side quests are completed.

• Let the story progress, but the player won't see the pieces of dialogue that related to the incomplete side quest.

• Remove the side quest from being accessed or remove a story arc. (or replace them with different ones.)

I hope this helps in ordering your thoughts in your non-linear narrative.

In a lot of ways, the ideal non-linear game is a game design symphony. That may sound grandiose, but I don't mean it in a bland, broad sense. I mean that the game is a tightly built set of puzzles and designs, all interlocking and building on one another into a grand finale that ties everything together. The design is the symphony. The game is the orchestra. And you, the player, are the conductor.

I'm basically making a non-linear game similar in effect to Oblivion/Morrowind. There is a main story arc, but you can choose to start or drop it at any time and you can recruit up to 7 other team members to take with you on this journey. As a result, you can get close to some team members but not others. There are sidequests they all can take part in or not. The ending of the game and their future destinies rides on your relationships with them. It is a pain-staking task to keep track of the myriad of options the player COULD choose. So what I do is I literally spell out for myself in a Word document all the possible choices you can make with each character. Then I take EACH quest that could utilize said character and what choices would effect that chracter. Then I write the end game result based on a single deciding variable that gets added to or subtracted from based on your choices. So if its between such and such range, this happens at the end, if its in 'this' range, this 'other' thing happens, etc.
Now when I go to finally program this all out, I'm starting from the beginning and working my way to the end in chronological order. The style of writing will flow better that way since I'll be working with the relationship with the characters and have it grow in my mind as it grows in the game chronologically. Seems reasonable enough to me.