Most every campaign I run, be it fantasy, modern, or sci-fi, I use what I call a sandbox with a plot. I generally handle all my settings where there is one over-arching "theme" with a couple major plot lines, several medium plots, and a box full of minor "standard adventure" plot hooks. Meanwhile the game runs like a sandbox as far as the players are concerned. They get hints with bits and pieces in the news from "GNN" or rumors to the major plots, all in the back ground. Medium or regional plots might affect the players more directly, while the standard plot hook is a random "pick your adventure"... At the start of each session I give a hand full of plot hooks and adventure seeds. Some are passengers willing to pay a lot to "take me here.. it's an emergency.. which will lead to an adventure, or a stow away trying to escape the law, or... "you hear a rumor that is soooo cool you just HAVE to go investigate... etc... The whole time I'm using the typical encounter charts in the books for passenger/cargo etc... but sometime I just insert my plot hook as one of the passengers, or a cargo.
The players are free to chose what they want to do, and where they want to go. If they follow the correct trail of breadcrumbs they might find themselves involved in one of the major plot threads. I don't run my games to make them "the main characters" in a "novel" I'm creating in my head.. (one of my friends runs every single game like that and it gets old pretty quick...) but if they play their cards right, there is nothing preventing them from becoming embedded in a "main story line".
I'll give you a couple of examples... the "current date" of cannon mongoose... (read it somewhere in one of my books... still at work so I'm just not sure...) Is so close to the outbreak of the 5th frontier war, that's one of the major plot lines going on in the background. The news and other rumors just kicking up has the Zho's and the 3I in the very beginning of border skirmishes... Personally I "got over" the idea of the 5th F.W. in the late 80's, so I won't give it much thought as a GM.. it's just background noise for my players anyway. Another closer to home plot involves the Sword Worlds starting another skirmish/revolt, taking advantage of the 3I's sudden focus on the Zho's... which is in itself more background noise.. but imbedded in that background noise are several plot hooks the players can easily insert themselves into.
Another major plot hook is "there's something wrong with the xboat system" cutting off the core worlds temporarily from the marches. Some kind of super virus is disrupting the communication relays along the xboat route is what one player (corporate spy) has discovered. Is this the beginning of "The New Era" virus, or is it a Zhodani plot to disrupt important communications just at the right time? I myself as a GM haven't made up my mind. I'm not going to cause the cannon Universe to self destruct, but simply taking bits and parts from all the other Traveller themes over the years. Just enough to keep my players on their toes. In any case, a super virus wont have any effect on the players... just more background noise. And besides, they are currently in the Trojan Reaches anyway... But I'm leaning towards Zhodani hackers... or something similar.
But where my TU splinters off from cannon is in fact my main over arching theme. And I stole it off Babylon 5. "The ancients are returning" is my over arching theme. And I'm not talking about the Dryone. If there are currently 6 or so major species "today" why was there only one species "in ancient times"? Which is the blink of an eye in Galactic time. So I invented a revised past where the Dryone had a long struggle with another advanced race and eventually won, pushing this other race out of the picture. Now this other race is slowly coming back. They are generally hostile. In my rewritten history, the reason the Dryone transplanted humanity, was in fact to create uplifted, highly genetically altered cannon fodder. After many years of research, the ancient Dryone settled on ancient humans as the perfect spieces to be genetically manipulated. After the Dryone won the war they pretty much went the way of cannon. The surviving transplanted humans developed "as cannon". I simply invented my own "Why humans were transplanted in the first place". In any case this new race is hostile. There are no great armada's no massive armies, nothing you might see on the big screen... just small handfuls of a long forgotten yet powerful race slowly making it back to the scene. It is a very rough outline and the "final outcome" will take decades if not centuries in "real" time. So no real effect on my players or my game. But 3 out of the six players have already stumbled across and barely escaped the very first encounter with this new race. They assume they are the only surviving humans who are in fact aware that a "new race" even exists. And they have yet to tell anyone! :shock: lol.

BUT they decided NOT to go down that plot hook trail, and kept going down their current path... tracking down the co-owner of a family run design/shipyard/manufacturing corporation called "The Winters Corp" located in Glisten. 15 years ago...Brother and sister fought for control after dad died. Sister wanted to push advanced development/cutting edge stuff, Brother wanted to focus on simple cheep "for the masses" designs. Brother tried to kill sister and make it look like an accident by causing a "navigation error" in her"advanced long range scout" into the waiting arms of a bad guy, an Aslan Slaver waiting for her ship to come out of jump where the brother's virus programmed her ship to jump. After the unfortunate "miss jump" with no sightings or signals, He declare her legally dead, but he has had to wait 10 years for the declaration to be "legally final"... in the off chance she might be found in deep space etc.. After the 10 years he can have full control. Enter the party with only 6 months to go... The players are following leads which may lead to her rescue... if they don't get killed or enslaved themselves... Anyway, the players go the final clue on where they think she might be. If they find her and return her safely to Glisten before the "10 year" window expires, she will get full control of her fathers corporation and her brother will be in prison. If not, he gets full control... If they succeed, they will get a nice reward, worth the risks. If not, they will get 6 new plot hooks / adventure seeds.
The players were heading deep into the Trojan Reach when the game was suspended.
It was only last night when I got the "We want to play Traveller again" vote, so today I'm in a bit of a spin. I have to have things ready to go my Tuesday night... no pressure... lol
Try to reinstall the current plot, with new players and the previous player "ship owner" long gone, or reboot with all new characters. :?
Sorry for the length... past time for me to head home...Thanks for your input guys.