I'll start by throwing down my mod fantasy that's inspired by both EV Nova and Starfleet Command:
Upon reaching a station there will be a list of missions I'll be able to select from; some will pay handsomely for daring tasks, others will be low-risk low-reward and mundane. I choose one named "Investigate Distress Call" that will help me pay for that new weapon I've been eyeing. It has me warping two sectors over into an unpopulated area of space where I find a damaged ship floating with debris around it. Upon clicking the ship, the mission begins to load. I find I'm on a large map and cautiously venture toward the center where I find a crippled ship, at which point my close proximity to the ship triggers one of several events depending on the mission:
1. Pirate raiders spawn nearby accompanying the text, "Arg, I hope ye be more cooperative than yer friend. We had to teach him a lesson. Hand over some credits or we'll be teachin' you too". An options box appears with text choices to either give the pirates $3500 credits and leave peacefully (at which point the mission ends) or fight them. Not giving in to pirate scum, I choose the fight option and brace myself for a wave of pirate frigates. I can either attempt to flee or defeat the pirates and recover the loot in the damaged ship's cargo hold as an additional prize.
2. I begin to scan the strange alien craft, which appears to be deserted, and detect some loot in its cargo hold. A larger hostile alien craft then spawns with some strange language and I must either destroy it to recover the loot or flee, leaving the loot, but saving my life. Either results in mission success & payout.
3. A Hedgemony fleet spawns south and Tri-Tachyon fleet spawns north. A few seconds later a text box appears saying, "Unknown vessel, this is Hedgemony captain Hank Taggart. A Hegemony patrol answered our distress call, but we're outnumbered. Will you help us?" I'm given the option of joining the Hedgemony fleet or Tri-Tachyon fleet. Regardless of the decision I make, additional ships will spawn on the enemy side to even the odds.
4. Something amazing happens, just think of the possibilities!
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Ultimately, this allows missions to be scripted using events or countdowns to trigger events or countdowns.
You have a trigger:
-countdown timer
-ship proximity
-specific ship destruction
-etc.
That triggers one or multiple events:
-countdown timer
-ship spawn
-text display
-options box with text choices
-etc.