I have been reading in this forum for a bit and see that there are many many good ideas, but nothing is moving here. So to get things started I wanted to give you some guidance in terms of structure and workflow.
Now I am not an experienced writer. I loved writing since I was a child, but only recently I took it to the next level, when I was recommended a book about screenwriting. A very good book - some even call it the bible of screenwriting. This said, I'll be happy to learn more about this from people with experience in this area. Otherwise I will try to advice and guide you as much as I can.
Ok, first of all I want to say some things about the nature of stories.
- Most important: Stories - books, movies, games, tales etc. - are there to entertain. If you didn't realize that until now take the time and think about it. They are purely to entertain. If you want to educate there are other formats for that. You should always bare this in mind when trying to implement out-of-the-ordinary things, like letting a main character die in the middle of the story, or having no antagonist.
- You have to consider the differences between a movie, a book and a game. Books usually live from the insight in the main characters thoughts. You don't have that in a movie. In a movie you can only _show_ emotions, thought and so on, you cannot describe them. (That is why a movie adaption of a book should be considered something else than the book itself. Sometimes it's impossible to make a movie out of a book. Best recent example: Twilight. The book lives from the insight in the main characters thoughts and feelings. In the movie the character just appears to be stupid, being dumbfounded and openmouthed half of the movie.)
In games it is a bit different. Essentially it is like in a movie: you can only show what feelings characters bear, what thoughts they have. But you do have an influence on your main characters choices. Choices are the expression of thoughts/feelings/attitudes, which means you have an influence - and therefore a limited insight - on the characters thoughts and feelings. We should consider this later.
Now to the structure of a story. I guess you all heard in school about first act, second act, third act, climax, decline and so on. Those structures haven't been invented to torture pupils. Seriously.

They are not rules either. They are proven structures that worked for centuries and still do. They are a way to keep the audience's attention, to keep them hooked.
In a movie a single act usually spans over roughly 30 minutes, giving a 120 minutes movie usually 3 acts. Each act has it's own climax. Consequent act-climaxes haven to be stronger each time, making the final act's climax - which is at the same time the story's climax - the strongest.
Each climax has to bring a change that majorly impact's the story. All climaxes' consequences may be reverted in following acts - except the final climax. It has to bring the greatest change, which _has to be_ irreversal. It is the ultimate consequence, the cumulation of all the main characters choices, and for it to have a meaning it must not be reversible.
Acts are made out of sequences. Sequences are made out of scences. Scenes are made out of beats. Each of those elements has to bring a value change, here ordered from strong to weak. (climax > sequence > scene > beat) Now telling you about beats might be a bit too detailed, so I will only outline this roughly.
- Beat: An interchange in a scene. For example take two people. They are talking, but suddenly the start arguing about something. That would be two beats. First they are talking normally, then in the next beat they argue. The value change here would be e.g.: relaxed -> upset
- Scene: A sequence of beats that bring a stronger value change. Imagine those two people from my example start fighting. Value change e.g.: peaceful -> violent
- Sequence: Some scenes that serve a common purpose. In my example there could be some more scenes about those two guys, who might have been friends in the beginning, but over the course of scenes this friendship grows into hatred. Value change e.g.: friendship -> harted
- Act: The climax of an act bringts the greatest value change. In my example there could be more sequences which deepen the harted between the two former friends. Ultimately one kills the other. Value change here life -> death.
This might sound very movie specific, but it is true for books and games as well. All those elemnts need to bring a value change, otherwise they have no purpose and can be cut without losing anything in the story. The rising in importance of the value change is to prepare the way to the climax - a tension curve. After an act's climax you have to start slower again to give the audience a break to recover - otherwise they would wear out and the next act's climax wouldn't be as effective anymore.
A story has to be progressed by decisions. Random events progressing the story take out the meaning of it. There might be random events, of course - even more than in reality - but the story has to advance as a reaction to the main characters decisions.
How does the story start? The so-called inciting incident set's off the hero on his journey. That it true for every genre. The inciting incident can be something random, but it has to turn the hero's world upside down. Then onwards the hero struggles to restore normality in his world (don't take world to literally, he doesn't have to rescue the world for this).
It is in human's nature to try to find the way of least effort. In this case it means the hero will try to restore normality with the least effort at first. But the outcome of his attempt is different than he is expected - maybe he made the situation even worse. Over the course of the story the hero takes ever stronger messures to restore his world, ultimately leading to the strongest decision in the story climax.
The story climax always has to be a clear decision between two strong value charges. E.g. be cowardly and run away or finally stand and fight - and risk dying.
The audience needs an antagonist. There doesn't have to be a super bad villan, the evil mastermind, but the audience needs something or someone to focus on. Take The Matrix as an example: All agents are bad and want to kill the main characters. But the main antagonist is Agent Smith. Even though he is not superior to the others he is the one antagonist that we will remember.
Antagonists are not evil. They are always doing the right things - from their perspective. It might be a twisted, evil perspective, but they have to believe that what they are doing is the right thing to do.
Finally some words about the main character:
Characters possess dimensions. A dimension is a characters attitude to a certain thing/person. E.g. the main characters mom is always lovely to her son. We never see any other attitude from her and that is fine. She is just a unimportant side character and not important for the story. The more important the character - the more often they appear - the more dimensions they need. The main character needs the most dimensions, so the audience can identify with him the best. E.g. he could be nice to his mother, loving to his wife, dangerous to the antagonist and violent to someone else. I don't know in how far this is realizable for the main character in a game, but it is true in a game for other characters as well.
For the audience - or the player - to identify the character they need to see something in him and think (deep down below): Hey, he is like me. E.g. the main character steals something and has a mighty bad consience afterwards. Even though he has done something bad the audience will sympathize with him, because he has a bad conscience. They will think "it is the same as me, when I took xyz". We have to make the audience sympathize with our maincharacter - or it wont work out.
Now I am sorry you had to read all this about story structure, but it is necessary to know about this. I know I have the habbit to explain things quite complicated, so please ask questions!

If you want to read about this in more detail I can recommend you the book I read.
Now about the process in our writing department:
First of all we need an idea what our story should be about. When we have that we need to start creating scenes, working our way through the story until we discover what our story climax will be. Then we have to work backwards to correct the scenes before so the story climax works and there are no logical gaps etc.
In our case, because it is a game, I think there can be several story climaxes, as I imagine that the story evolves like a tree, depending on the players decisions.
Be aware that we will have to create TONS of scenes and most of them will be discarded. We will have to select the very few that are high quality. As mentioned in that book, good writers know that 90% of what they produce is merely of medium quality. We have to find those 10%.
All the while we will have to create our world. That is: work out all the ideas you have. Create events in the past, create a past for characters. All this has to be written down and worded in as much details as necessary. We will have to create tribes, customs, clothings, all that stuff which can be used as references in the actual story.
We will have to have perfect knowledge of our world so we can create a waterproof story.
We will have to create the main arc - which will most likely fork - and subplots. They have to be connected, at least at one point in the game. Otherwise the subplots are meaningless. A subplot could for example be the lovestory of the main character with someone else. Ideally they all climax in the story's climax - or at least in an act's climax.
This is what I suggest we do know:
We have to keep track of the ideas and background information. A good place for that would be the wiki. I suggest we post proposals in this forum, marking it clearly like "[Proposal: Act/Scene]" or "[Proposal: Background/Event]" etc. In this thread we post the idea and the discuss about it, refine it and finally store it in the wiki. In my opinion there should be one or two people who take the final decision, so the discussions don't go on forever. (We can't put all ideas in the game. Remember, it's all about entertaining the audience.)
This will be quite a patchwork process and require a high collaboration. I'd prefer this collaboration to happen in IRC and to post only the results in the forum, but I don't think this is possible with timezones and current user activities.
So this is where my "experience" ends. For my private story I had an idea what I wanted to happen in my story - I had a rough outline, so I knew my acts climaxes and could work towards them. We have nothing right know, except the setting. We need to decide what this story is going to be about, and then start working from there.
That was hell a lot of text and I am sure I still forgot about important things.

Please let me know what you think of this.