If you want an overarching more-or-less-linear narrative, I would go with:
- The game has a global timeline, or several global timelines in parallel. This allows the world to change permanently in response to key plot events. (E.g. Skyrim, Final Fantasy 7)
This means that you organize organize your design process by making a timeline. ...Flowcharts are often preferred by arty, visual people, while spreadsheets are often preferred by people who like history and math; either could work fine for your game concept if I'm understanding it correctly. Do you want a more detailed description of how one of these methods would be used?
Global timeline, as in key events that affect all the cultures present within the game world, or at least very significant ones. Correct? A single player choice may create a domino effect that sets off a huge change in future occurrences. Less significant events may also affect minor outcomes, say for example anything between individual characters or any small factions or groups. Yes, I've considered a timeline, although the programs I've found all seem to be rather restricted. It would be interesting if I could lay out even the most minute of events. Like a zoom function, scroll out to see the largest, global events. Scroll in to see small character or group events, even further in to see dialogue events.
I may still try the wiki, as Servant mentioned, I could host it through my own webhost. Multiple methods may work well together. A flow chart sounds wonderful, but it requires a great deal of effort to complete. A spreadsheet might be my best option to begin with, from there I can dedicate the time to work on a very well planned (and very long) flow chart. I would very much appreciate an example if you had one, that would help me to an enormous extent. I've been looking for references for the structure of this process.
Thank you very much for your help so far, sunandshadow.
Personally I think the problem with flowcharts (or mind-mapping which is like flowchart lite) isn't the effort involved, but rather the fact that there isn't a really great free flowchart software. It can also be challenging to get all the information back out of both flowcharts and wikis (when you want to copy and paste substantial amounts).
Anyway I'll just describe how one would use a spreadsheet to keep track of a game with a global timeline. First of all you want to make sure you are using a free spreadsheet software so that every team member can use the same one, as errors can appear if you're trying to use two or three different softwares to view and edit a spreadsheet. I personally recommend LibreOffice as an offline solution, but Google Sheets has good points as an online solution. Many wiki softwares include the basic ability to make tables but don't have more advanced features.
Second you want to brainstorm a bit about how to group your information. If you have distinct locations in the game, it may work well to have a spreadsheet page per location. Another possible way to break things up is by faction if factions are really important to the game, or by viewpoint character if you have a limited number of viewpoint characters with distinctly different options within the game. Then for that page each column would be an NPC or other source of information like an interactable object (or location if that's not what sheets are). The rows would be numbered for the global time increments, and then you can add sub-rows for quest-local increments. Then the cells would each get an ID number along with a dialogue exchange or a description of an action a player can take and the consequences that would result. These ID numbers are very important - you use them as a check-list when editing text before committing it into the game, or assigning them to a voice-actor, and when assigning scripting to NPCs and objects withing the game, etc.
Example: While the development documents for Skyrim aren't publicly available (as far as I know, anyway) players have reconstructed the quest stages by looking at the programming. For minimal spoilers, here's the first main quest segment from Skyrim. The part I'm talking about is at the bottom of the page where there is a section called Quest Stages and a table labeled Unbound (MQ101).
http://www.uesp.net/wiki/Skyrim:Unbound
Similarly for Final Fantasy players have reconstructed some of the quest stages and flags by looking at the programming. I couldn't find an easy-to-understand presentation of this data though. Basically you'd have to look into the Black Chocobo Save Game Editor, the Game Progress Section and the Test Data section are both relevant.