As the player explores the galaxy, it will be important to hold territory and have bases somewhere nearby so you can respawn in the event of death.
The first thing to understand about the galaxy is that only the area around the player is active.
The other areas are in stasis until the player arrives.
Agents do not actually attack stations or plow through regions as they approach the player. They are nothing more than a map indicator until they get within range of the player.
To hold territory, the player must advance into new regions, destroy enemies and build stations and allies.
Stations should have a factory. This acts as a respawn point if the player dies, and acts as a collection point for your allies to collect R.
Make Bases
The best way to hold regions is to place a reasonably affordable base (with a factory) and a few cheap allies in each sector. Allies will collect R, bring it to the base, which will build more allies.
Make a base and a couple cheap allies to collect resources. Release these ships from your fleet and move on. They will harvest, build, and protect that territory from invaders.
If an Agent passes through an area, your bases will be destroyed. If this happens don’t worry about it. Keep your bases cheap enough that they can easily be replaced.