I'd like to see something in the likes of the Elder Scrolls.
I would too, sort of. At least in morrowind (game three of the Elder scrolls series), the "Stories" you come across that are unrelated are all scripted plot events and quests. Other than that, the world is devoid of life. I don't really like the "quest system" in which people give you stupid errands to run in exchange for some random trinket you needed for some other guy's quest. I never finished Morrowind because I got tired of running around.
Have you ever played an old game called Darklands? The game was mostly text-based, with real time graphical combat, but I loved it's plot. It's based on folklore of medieval Germany.
The game never even told you that there was a main plot, there was just lots of stuff to do, and the natural flow of the game guided you to them. Take one of the 'early' main plot quests: clear a demonic infestation out of a mine.
Also, if I may digress for a bit, the "quests" in darklands may or may not be assigned by anybody. If a robber king is terrorizing a village, you cn go to the village and try and find someone who will pay you to kill the guy, but you can also go and do it (and receive the thanks of the people).
Your regular business, which involved cool stuff like stumbling upon a merchant being attacked by thieves (you could step in and help, and then upon beating the theives, steal everything the merchant had "in return" for saving his life. There are I think eight or so different outcomes to that one situation), would lead you to know about the plot. You would hear rumors about the mine from people you encountered, and then, if you were interested, you could seek it out. On the way to mine, there might be a witches' altar, which, if you purified with a holy ritual (or just by tearing the stones down), would bring the wrath of the witches down on you, which is sort of the next quest. That's just one way it could happen. All the main plots are connected somehow, and you can do them in any order (although there are easier ones, there is no "right" order. It makes sense either way)
Also, if I may bring up another game as an example, in Elite: frontier, there were main quests as well, but if you didn't take the time to do them, someone else would.
Let's take these two ways and apply them to Charon system in a hypothetical, more dynamic future Transcendence with a gate network.
You're flying along, and you stumble upon a freighter getting attacked by pirates. This situation may have arose by itself, and the game just watches for situations like this to apply the plot, or maybe it's scripted (although you have to allow for things like the player just ignoring it or deciding to destroy both parties).
Anyhow, once the pirate is dead (or you are exploring the wreckage of the freighter), you get thanked by the freighter and he tells you to mention it at the next Korolev, or next time you meet a freighter pilot in a bar. You dock at Korolev, and they say, "thanks for helping out our pilot, here's some cash/goodies. Those pirates sure are getting bold. I hear they have control of a whole system somewhere in the Hypothetical sector."
Thus the player is alerted to the plot event. Alternatively, the player could find a partial map to the system in a destroyed pirate cache, or follow a careless pirate back to the system.
If the player visits Charon and chooses to leave and not come back for a long time, or reaches a point sufficiently far "ahead" of Charon without clearing it, he may hear about how Korolev and CW forces joined up and led a strike force against the pirates and won.
I'd also like kind of a dynamic plot in later systems (Ares vs. Commonwealth) you could have Ares and CW fight it out for systems, with the front lines changing all the time. Basically a whole bunch of ships from both sides enter and fight to the death. Whoever wins controls the system.
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I ain't trying to diss your hard work and effort)
