Please pardon the double-post.
I'm wondering where I should go with First Contact. I've got a basic idea laid out, but I'm wondering if I should have planned more as to the game itself; no map of the ship yet, only the most general idea of who the enemies are, etc. Not sure how to decently craft a plot, either. Whenever I do, I end up comparing my ideas to the books I read, and they don't hold up. There's rarely the intricacies and overall connected-togetherness.
Well, for starters, a strong setting is important. If the players are spending a lot of time in the ship, you should have at least a good idea of several major locations in the ship ahead of time. You can come up with more as the plot demands. As for Plotcraft, it sounds like you should experiment with the art of the Plot Hook. As a GM, you don't need to plan every intricacy out ahead of time; in fact, that's often a bad idea, and leads to railroading! You just need to create characters and motivations, and let events unfold organically, based on the players' actions.
Create a setting. Create a number of NPC Entities, be they religions or empires or cosmic forces or individuals or whatever, and polarize them. Give them resources, personal goals, and plans by which to achieve their goals. Set some of them at odds with one another; give some of them goals that clash. Then lump them into your universe, let your characters know the surface details, and then have them make their characters, and encourage them to have ties with one or more of these NPC factions or entities (they can be friends with these entities, or enemies, or might owe them a favor or be owed a favor, etc). Then, if you drop enough Plot Hooks for the players to get involved in these factions, and swept up in their plans, they'll react, and suddenly you have a plot! The players will let you know where they want the plot to go, and they may surprise or inspire you with an endgame you didn't expect.
If you'd like a nice, simple structure for writing a compelling interactive plot for a game, you could do worse than familiarize yourself with Minimus. You don't have to do things the same way, but it's a great base to adapt a storytelling structure from:
Linko