Foundry start
Recently I started to work a little bit on a mission in Foundry in Star Trek Online. While I generally like the toolset from an initial view, I have still hesitated a bit. I am not a bit Star Trek fan and do not have detailed knowledge on much of the Trek lore – if I do something I would like to keep it consistent with the general world set up.
Either way, I have started to work on a mission and similar to a few of my story arcs in City of Heroes Mission Architect, I used my existing characters as inspiration. Since I usually have some thought or idea what my characters are I have found this to be helpful to make up some kind of story.
Foundry mission editor
While the Foundry seems to be a pretty decent tool to create missions with, neither it nor Mission Architect are good tools to write a story in. Text editing is very basic and one does not really have any support to organize the story writing – what are the characters, their motivations, background info, locations, timelines etc.
There are a number of different tools around to help with writing stories (novels, screenplays etc) which may be of some help, although most of these are commercial offerings. Personally I have settled for using a mindmap editor to help with the story/mission writing, Freeplane. I use mindmaps at work and find tools to create those to be quite useful.
Any kind text editor or word processor can be used also, but I like the way I can work to organize my thoughts and ideas through the mindmap. One useful feature that should be considered for text handling is that the tool has a spell checker. I have seen a few spelling mistakes in Foundry missions, it could certainly lower the overall impression of the mission if there are too many.
Using Freeplane to start organize the mission story
In a perfect world a lot of the work could be done outside of the Foundry mission editor, before even using the editor – most of the story writing could be done that way. However, for that to be practical one really need to be familiar with the Foundry toolset and perhaps done a couple of missions. When the toolset is new I find it more suitable to switch back and forth and be more iterative – work a bit in the mind map, try out a few things in the editor, back to mind map etc.
For example, I had to change some of my initial locations I had planned – they were not available for players to start from when I tried to set it up in the tool. I see this mission work as learning how to use the Foundry and see how I can combine it with handling in Freeplane.
I expect this to take a couple of weeks; I will perhaps spend a few hours per week on this and from my experience with Mission Architect it can take quite a bit of time to get a story arc to a stage where it feels reasonably good and ready to be exposed to others.
A ding world 
You’re on the right track writing your mission outside of the Foundry tool. That’s one of the main tips I’ve heard from interviews with Cryptic staff. Apparently even their in-house development tools don’t have spell check either and they do their writing outside of their tools and copy/paste stuff in.
Learning what the Foundry can and can’t do is definitely the hurdle there. Even doing a basic mission back on Tribble a few months ago I ran into some problems being able to do what I wanted, so understanding what features are available will definitely help keep from writing something that you can’t actually build.
Good luck!
It is the same situation with Mission Architect as well – the tool itself is not good for managing the mission text and can be cumbesome to manage only in the tool itself.
MA editing is slightly better I think, at least you see what the size limits are sirectly, you have a lot more variables and meta information to include (or maybe Foundry has some of that, just not has not seen any documentation for it) you have a bit of a preview directly.
Still it can be really difficult to manage. In the MA case you also have all mission data in a local text file, but the format is not something you would normally want to edit in directly, as you could mess things up if you are not careful.
Learning what you can do with the tools is certainly something that will take time and definitely why I think some iterative approach is needed. Ideally it would havew been nice to have the whole world available also as if you were in game, e.g. check locations, see what descriptions are for different words and characters, look at how various places have been designed so you can be consistent with any things you do yourself etc.
Since you are logged in, but not actually in-game when you are in the editor such things also take extra time logging in and out, unless you have a second account.