Message: The [Regiment or Republic] has noted some unusual signals buried deep within the output of the newest brand of Delta Inducer. These signals appear to be designed to trigger a dependence on the device for sleep. The [Regiment or Republic] fears that the corporation responsible [corporation name] has even more sinister plans in store for this device which has become vital to our national security. This mission requires a special operative, which we will provide.

Mission details: Go to the corporate headquaters of [corporation name], located at [name of high-tech system in the Corporate Confederation]. Land. Our operative will then exit the craft, extract the CEO, and return to your craft with our target. Security will no doubt be alerted to his absence, so after you have completed your objective, take off immediately and head for [Regimental or Republican] system. A flotilla will be awaiting you. Even if a battle ensues between the flotilla and corporate security forces, go directly to the nearest starbase to deliver the passengers.

If Mission achieved:

Regiment: Congratulations on the success of your mission. After a long discussion with the CEO, we discovered that we were mistaken. The malicious coding, in fact, never existed. You are sworn to secrecy as to the details of this mission, and are to discuss it with no one. Thank you. You are dismissed. (adds rank advancement points) (in the next issue of the Regimental news] The Regiment has signed a landmark agreement with [corporation name]. This deal will save the Regiment billions of Credits over the next month alone. The Regiment has called this "the beginning of a new and promising friendship with businesses everywhere."

Republic: Congratulations on the success of your mission. The CEO currently is awaiting trial in a holding cell on Kal'Foran. Good work. (adds rank advancement points) [issue after next of the Republic newspaper] FAMOUS CEO CONVICTED IN TRIAL: The CEO of [corporation name] has been found guilty of [insert technical sounding crime names]. Her plea for mercy in the sentencing hearing apparently struck a chord with the jurors, who saw fit to recommend a sentence far short of the maximum available. She will begin serving her sentence on [random location in Republic].

If Mission is failed:

Regiment We were disappointed to hear of your handling of this incident, [current rank]. Because of your blunder, the Republic instead has brought this criminal to justice. We had sought to capitalize on the resultant publicity. Your handling of this won't be forgotten. (deducts rank advancement points) [Republic newspaper article released]

Republic Due to your poor handling of this incident, the Regiment reached the CEO first. They have signed an agreement with [corporation name], and are now providing protection for her. It now appears she will never be brought to justice. We are severely disappointed in your actions. (deducts rank advancement points) [Regiment article released]

Trigger: Time and allegiance.
Nation: The Remnants of Imperia
Offered to: Imperical officers of sufficient rank.
Ship/Equipment: For this mission and for this mission only, you are given a specially equiped, specially manned ship.

Message: "Want to deal a critical blow to the Republic's pride and resources?   We thought so.   The relentless persecution of the true rulers of its territory will end with this display of our might: we have gained access to critical information concerning the jumpgate to the old galaxy.   We will strike hard, erasing the jumpgate and the security of those who fights for the Republic in one fell swoop.   Though the security will be lax for a few instants during the shift change, be warned that this is still one of the most heavily guarded targets in the Republic.   A carefully trained team has been assembled to take the jumpgate out.   You are part of that team.   Whether you live or not, you will be a hero to your people and remembered forever."

What happens next:
    (this narrative was written to convey what I had in mind: the gameplay won't likely be this rigid)
Cast of characters (with stand-in names):
You [commander]
Defoe [weapons]
Jaquar [tactical awareness]
Clorinthe [engineering]

[Jaquar]: Greetings Commander.   This is Jaquar, your second in command and tactical awareness officer.   This is Defoe, your weapons man.
[Defoe]: Good to meet you, Commander.
[Jaquar]: Rounding out the crew is Clorinthe, and she'll be the engineer on this trip.
[Clorinthe]: A pleasure.
[Jaquar]: Your reputation proceeds you, and I think you'll find that members of this crew are quite deserving of their posts.  There is nothing ordinary about this mission.   We are specially equipped to destroy a heavily defended target and get out alive.   Defoe, inform the captain of the weapon's payload.
[Defoe]: Thank you, Jaquar.   The weapon in question is a unique artifact smuggled from the old galaxy.   It has the potential to destroy the jumpgate and her defences, and could easily spell the end for us as well, if not for the careful timing of the attack.   The timer on the device will give us just enough time to hyperspace out safely.
[Clorinthe]: And I'll keep the drive working long enough for us to get out of that hell.
[Jaquar]: Our time is short and our launch window is upon us.  Clorinthe has the coordinates locked in.   We hyperspace at your leisure, Sir.

In the area of the Jumpgate:
[Jaquar]: All systems go.
[Defoe]: The artifact is prepped and primed.
[Clorinthe]: Hyperdrive functional and locked onto our force randezvous point.
[Jaquar]: The advantage of surprise is ours.   The security forces are not reacting to our presence.   I suggest we launch the strike and leave the area.   We must time our departure so that we may confirm detonation, but other than that, all command functions are at your disposal.
[Clorinthe if you attempt to hyperspace]: I'm sorry, Sir, we need to confirm detonation.   I'll handle the timing.   Don't worry.
You launch the weapon...
[Jaquar]: Something's wrong, the jumpgate is energizing and moving to meet the approach of the missile.   Get us out of here!
[Clorinthe]: Hyperdrive countdown already engaged...
[Defoe]: The artifact has been hyperspace away!
[Clorinthe]: They knew we were coming!
[Jaquar]: I'm reading large clusters of jump-points.   We've got incoming ships.
Seconds pass.  The countdown for hyperspace ticks down...
[Clorinthe]: Damn!   They've jammed our hyperdrive.   Trying to get a fix on where the jamming signal is located...
[Jaquar]: Try to make it to the jumpgate!   We can cut through the interference if we use it to boost our drive!

If you reach the gate in about ten seconds:
[Clorinthe]: We're out of here! (hyperspace)
the fight will follow you, but you'll have more of a chance

If you don't reach the gate in time:
Twenty or thirty seconds of hell ensue.   It's you against an army.   Defoe starts noting the percentage of your shields holding.   Only the smartest commanders will survive.
[Clorinthe]: Got him!   He's marked on radar and on visual.   Knock that bastard to kingdom come.
You pick out the ship by radar and manage to destroy the marked ship.
[Clorinthe]: Hyperspacing in... (counts down with hyperdrive)

The Aftermath:
[Jaquar]: Sir, I think it I speak for all of us when I say it was a pleasure serving with you.   A pity none of us will never see each other again.   In the meanwhile, Imperian command has given me the duty to inform you that we have all been given commendations for our bravery and our original ships await us at port.   Clorinthe will take us in.   Your next mission, of course, involves the hunt for the mole who gave us up.   Details await at your ship.

Trigger: Location (a specified system in the old galaxy)
Nations: Any.
Offered to: Anyone in the system.
Ship/Equipment: Any.

Message: [via radio] "Assistance requested!   Assistance requested!   It... She's loose and she's killing everything!   Assistance needed at Citadel Station!"

Events if you approach Citadel Station: Just as the station becomes recognizable, it explodes.   The wreckage contains: A saucer-enclosed grove of trees identified by a stencil on its side as "Delta" (the grove is too big to be scooped, but may be fired upon), an escape capsule, high tech goods, computers, and personal weapons.

If you pick up the escape capsule: A weary traveler boards your ship requesting to be taken to the inhabited planet of the system.   He offers you more than a fair price for the trip, and tells you a strange tale of a mad AI on the way.   He also advises that you blow up the grove and sift through the flotsam of the station for various goods.   A monetary award awaits you on the planet as well.

If you blow up the grove: You receive a boost in reputation in the independent worlds of the old galaxy.   The award value increases slightly.

If you blow up the escape capsule: Your reputation suffers a slight decline in the independent worlds of the old galaxy, as it would anywhere for shooting an escape capsule.

If you ignore the event entirely: Predictably, nothing happens.

• The Nation of Reoliscan has an extremely well developed transportation system of these jumpgates, and has decided to wait and see if newer hyperdrive technology is as reliable as the old tech. of jumpgates. Of course, hyperdrives do have certain advantages, and the Reol are standing by to produce them. Therefore, currently most Reol ships don't have independent jump capability, but a few of the more massive ones have jumpgates attached to the ships' frame.
• Most humans in this new galaxy use still have jumpgates between major political, industrial, and military centers, but are beginning to rediscover the secrets of the hyperdrive (their progress being up to about a military class .5 or so...) and are slowly deconstructing their networks.
• Most small ships use a fastdrive for interplantetary flight, which has the same pitfalls of the old torus jump drive (starquakes, etc.). A delta inducer is offered as an alternative for ships to large to use this technology.
• The Augurs has designs for more advanced hyperdrives and for a wake disrupter for jump drives (so starquakes will no longer happen). They sell these for immense profit, to help fund their incursion into the new galaxy.
• When the Augurs first offer the wake disrupter for sale, many don't believe them. The Reol decide to wait and see (having unexpressed doubts about the Augurs, not to mention their wake disruptor)... until a few starquakes occur.
• The Nation of Reoliscan never does switch over to hyperdrives, but they eventually require the wake disrupter on their fastdrives.
• The Solnaria Factions never adopted the fastdrive (thus no need for the disrupter device), and eventually switch to/steal the better hyperdrives as they become available.
• The Augurs are by no means good guys... they just need the cash for their planned voyage to the new galaxy, and the wake disruptor is one of the unique items they have to offer.
• Also, though the Augurs put up the facade of being a high-tech nation (and some are fooled at first by a couple of unique gadgets they have), soon it is realized that they are not all they claim to be...

• Also, I suggest a contest in my drive section. I'd like to not that although the Augurs (again) come out in top on this one, it's the exception: The Augurs have a wake disruptor, a few ship designs, and a good hyperdrive. 'Tis all. I've just written about their advantages first... I will get around to their disadvantages.

• Kind of a battle for souls starts between Augurs and (humans of the) Reol faith after the Augurs enter the new galaxy. It should be interesting...

More loosely structured than most sub-plots, there'd be no real mission to accept.   Just a mention of the reward in a newsmag as well as where to go to claim it.   After that, it's up to the player to sort out clues left on several planets to determine the true location of the Sol system, sorting through several false claims along the way.

Earth itself should be a fairly unassuming as in FFE.   You could take this for a tribute to the Foundation Series.