Weepul, you're gonna have one heckuva time with that one. I, personally, would absolutely love to do a submarine plugin for Nova. Hmm. Maybe I can convince BariSaxGuy to do a couple other graphics.... hehehe...
Y'know, Arthur C. Clarke did a great short story about the medium-near future, called The Deep Range. Weep or Legion, you really should read it. Two reasons: 1) it's a great story, and 2) it'll give you a lead on an absolutely astounding storyline. Here's the gist of it, but you still oughta get the book (it's included in his anthology Tales from Planet Earth , published by Ballantine. Sometimes, I think those guys have a monopoly on SF books...).
In the future, humanity was running out of food. Then, we went back to our true home, the home of our ancestor's ancestors: the sea. We designed grids of electric generators (a possible explanation for the edges of the system, and hyperspace) to corral our new cattle, the whales, and prevent the sharks from attacking them. (Obviously, a lot of parallels and analogies will be made to the Old West.) Our faithful companions and comrades-in-arms are the dolphins and porpoises, even more intelligent than the dog, and capable of assisting us in our most desperate battles. However, there are still vast stretches of ocean with no corrals: the sea is a pretty big place, and stationary generators are expensive. And the whale pods sometimes stray into these unprotected territories, or the sharks will slip in when the gates are turned off to let in the whales. This is the job of a proud few, who protect man's source of livelihood and food.
Now, the story followed one guy in an incredibly souped-up minisub (which, from the picture included in the book, looked rather like a very big and very dangerous spearhead with a pair of switchblade knives extending at about a 60° angle forwards from the stern of the ship), who had to protect a pod of whales from a Greenland Shark, a newer, larger, and much nastier variant of shark, not much smaller than a Blue Whale calf.
As to how the plug is set up, the systems could be laid out in a grid, and named according to coordinates (40°W, 15°S), and they could also vary in depth. If they are close to the surface, they would be a pale cyanish-blue color. If they're really deep, they'd be very very dark blue, almost black.
While you're at it, make the sea life realistic. A Lion's-Mane jellyfish can't survive much below the surface, but an Anglerfish can't survive much higher than the seafloor. You might even have the occaisonal lobster or crab shell.
As to mining, there might be a way to rig it so that just having an asteroid scoop would slowly give you cargo. Don't think there is, but it's worth a shot. People have dreamed about processing seawater for minerals for a long time. Of course, one of the most common materials will be salt. There might be some little colony or something that's based in fresh water, where salt will actually be valuable.
I think this could be an alternate-SF story, where space travel never really became practical. Of course, you could discover an alien starcraft on the sea floor... That'd be good.
I could really have fun writing this one, and I've been kind of playing with the idea for a while. Again, I have two problems keeping me from making this plug: 1) I'm already working on the Ages Trilogy, and 2) I'm worthless at graphics.
Oh well. If anybody actually takes this idea, post about it, I'd like to know.
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“You’re only given a little spark of madness. You mustn’t lose it.”
-- Robin Williams