Actually, the best advice I can give ya here is to -not- get clear directions. The way I learned it was by just leaping in and exploring the files, tinkering with things, and seeing how they worked and what they did. It's a learning process.

For the very basics, though, to do quests and the like you'll want to snag core.cpk and extract it using an unzip program. This will leave you with two folders, data and content. Data is where all the numbers and scripts for the game are stored, like weapon damage, gear for ships, that kinda thing. Content is all of the audio/visual effects for the game such as the 3D models, textures for them, sprites for weapon shots, sounds, ect. For quests and a campaign you will therefore want the Data folder, then the Topics folder. This has all the files pertaining to conversations you have with people (and thus, the quests they give). This is also where I'd start to get your hands dirty; for instance, look at files for generic_quest_begin_tutorial; these are the files that handle the first quest Joe gives you.
The Javascript file in particular handles all his various quests and branching sections of conversation that he offers, and gives you a point of reference: you've done the tutorial quest before, probably quite a few times. You know how the talk goes... so when you look at the JS file, you can say to yourself 'ah, yeah, I remember that from in the game, I guess this is how they do that'. Just reading through that one file will be more tutorial than just about anyone here could give you, I think, because it demonstrates things like:
- How to set up multiple inputs so as to give the player a choice between replies;
- How to spawn objects in the game world, like Scurvy's ship;
- How to give items to the player, or take them away;
- How to use the State setting to set up multi-part missions.
Honestly, if you don't know JavaScript... you don't really even have to, unless you want to get into the more advanced pieces of modding. Just look at what's already there and make use of it for your own ends. It's like building with Legos; the best Lego creations are made using mostly standard 2x4 bricks that everyone in the world knows like the back of their hand. It's all about how you combine them in awesome ways. And the best way to start playing with Legos is to tear some stuff apart to get the pieces you need before you put it back together the way YOU want.
