The mission system in The Galactic Line is the foundation that supports the personal-level play. Missions give a reason for the ships to exist and travel, gives goals to the crew, and throws complications in that give texture to their daily lives.
Missions are built on the resource system. So let's talk resources.
The most fundamental resources are the tech level economy points. Currently called "T0", "T1", etc, these replace both generic materials and scientific research. You don't unlock a new kind of superconductor, you get a T2 economy point. And these points get spent on building colonies and space ships. Simple enough.
There are also a variety of resources used to balance the construction of ships and colonies. Things like power, administration points, etc. These create a terrain for the players to build a variety of different kinds of ships and bases in a variety of different circumstances. Mods or custom settings can easily alter the playing field here.
But that's local stuff. Why do ships run around the cosmos? Here are some small possibilities:
1) Local rare resources. However, mining or research colonies are a better long-term investment.
2) Temporary situations, such as negative space wedgies or plagues.
3) Freight. Shipping resources around.
But those are not really enough to sustain a proper mission system. They're very basic and either too boring or too unpredictable.
Instead, the most critical trick is that resources can be local.
Local resources are simply resources that are about or from a specific place. For example, if you scan planet X-9, you get cartography points for planet X-9 specifically. Not generic cartography points.
There are many facilities which convert resources. Normally this is generic resources, like a solar array converting administration points into power. But a residential block converts cartography points into colonists, and a trade center converts cartography points into investment. These conversions maintain the localness: feed X-9 cartography in, you get X-9 colonists and X-9 investments. It takes time: conversions take some time, gathering resources takes time.
If you want to build a colony on X-9, you use X-9 colonists and investments.
This means your chain is to spend time at X-9, then to spend time at a colony world (or start those conversions up and come back for them later), then back to X-9 to found a colony. This has a fair number of gaps in it that can be used by other kinds of missions, allowing for multitasking.
For example, a simpler use of local resources is scanning a sun or solar system in general. Solar readings of the star X take some time to gather. You might be able to do it simultaneously as mapping X-9, depending on your setup. Either way, those localized readings can be used in a variety of ways. For example, they can be baked down on-board, converted into generic astrophysics points over a month or two. This doesn't require you to be anywhere specific, and can therefore run in the background wherever else you go.
Astrophysics points and local solar readings can both be used on any colony with a lab to create T2 economy points. It requires either a lot of astrophysics points, or readings from a lot of different stars. Either approach will pay off in the long run, and can be used at any colony you think needs more T2 economy. Of course, it takes time. You could drop those things off at the colony you're gathering colonists and investments from, do all three missions at the same time. Or you could start the colony missions, leave a crewmember at each, and fly off to take more star readings.
You also don't have to use those mapping points to build a colony. You could convert them into T1 economy points in much the same way. So your overall methods and objectives are up to you.
This is called an "open resource chain": a variety of resources that can be knit together in a variety of ways. This allows for mods and alternate builds to integrate in at any level. The key, from the dev perspective, is that local resources create a reason for star ships to keep moving. Also, during the missions complications arise, which gives players an opportunity to have a personal scenario where they interact with a bunch of people.
The actual interface for this is via "missions". This is a dense and complex environment, especially when the player doesn't know precisely what capabilities are available in which places. Missions offer a method to organize that.
A selection of missions are offered whenever you go someplace new, by simply batching up possible resource transactions. You go to X-9, you see some missions for mapping X-9, some missions for scanning the sun or the solar system. You also see missions for refurbishing your engines, studying for promotion, and a bunch of other ship-centric missions.
You can create more missions if you wish to customize things. It involves interacting with people that represent mission options, I'll cover that some other day.
After mapping, you go back to a colony. The residential district can convert local mapping into colonists, so you get at least one mission about that... and you can choose to look for more if you want other options.
These methods allow the player to have pretty good options offered no matter where they go, and they'll quickly learn "gut instinct" mission chains when they see certain resources can be converted in certain ways.
Galactic Line's core gameplay is scenes where you get to interact with people in a rather open way. This gameplay about choosing destinations and missions is a setup to help that happen in a convincing way, because mission complications and alternatives offer a method to unify and connect characters, as well as give them something to care about and a background event the player cares about.
This allows us to sidestep the problem of so many continuous-interaction games like The Sims. The player becomes inured to the soft, indifferent day-to-day pressures and begins to aim at the edges of the simulation. That's why so many people try to murder their sims, or get a ghost baby, or whatever. It's also why Rimworld players tend to vivisect their prisoners.
But if every "day" the player actually plays through is centered around a specific mission complication, the player will have a goal, the characters will have goals, and everyone will have a reason to share the stage and connect with each other.
As a demonstration of this, think about The Sims. Think about those specific events where you were throwing a party. You were probably focused on your goals for the party. For some people, this might have been "drowning everyone in the pool", but for most parties it was about raising friendship ratings, providing enough food, achieving sims goals, and maybe hooking someone up. There's a drive to get the party "running smoothly".
Imagine if playing the sims was done with much lower time pressures, but you didn't play each day. Instead, you had a weekly planner and only played the days when something important happens. It's a bit like that.