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In my current game I found I had been infected with secret pirate bases on three of my colonies. I was unaware until I got a suggestion that I attack the hidden pirate base on colony X. I did some checking and found not one but three bases, two finished, one unfinished, on three colonies. So I gathered my assets and went on a pirate extermination campaign, taking them out one by one. I then attacked and destroyed the two known bases of this pirate gang, though apparently they have another. This was interrupted by a sudden declaration of war from some insectoid empire. I just paid them off rather than trying to fight them at the same time.

I've dealt with pirate bases before but never on this scale in my somewhat limited playing of the game. So the question arises, how do you discover these bases before they are finished and well entrenched? Do you just need to periodically check all your colonies? Keep an eye on pirate ship movements? Is there a technology that helps?

My usual practice for dealing with pirates is just to pay them off and let them live as long as they don't cause me any problems. I now many will disagree, but I find that less of a hassle than trying to exterminate them. Maybe I need to rethink this, though I usually don't have to deal with secret pirate bases.

In this particular case, this pirate group was on the other side of a friendly empire of like-minded humanoids, and I was paying a very low protection fee to them, like 98 units. They seemed harmless and small. When I attacked their two bases, I found out they were anything but small, and I was glad I had brought overwhelming firepower to destroy them.

If it makes a difference I play on full manual while receiving suggestions on everything I can get suggestions on.

I've dealt with pirate bases before but never on this scale in my somewhat limited playing of the game. So the question arises, how do you discover these bases before they are finished and well entrenched?

Periodically checking all of your colonies is the only sure way to find Hidden Pirate Bases and Hidden Pirate Fortresses. The easiest way to do so is to open the Colonies menu and scroll through looking at the facilities icons in the list; if you haven't built anything on the planet, then the pirate facilities will show up in that column. If you've built facilities on your worlds, you may need to take a bit more time and look at the facilities tab for those colonies upon which you've built stuff, though sometimes the pirate facilities will show up in the list even though you have things of your own on the world.

Rules for pirate facilities and influence:
Hidden Pirate Bases can only be built on colonies at which a pirate faction has at least 50% influence, and Hidden Pirate Fortresses can only be built at colonies at which a pirate faction has 100% influence and a Hidden Pirate Base. Pirates generate influence over a colony actively by raiding the colony, or passively by having ships in the vicinity of the colony (at a rough estimate, the region in which the pirates need to have ships in order to generate influence is roughly the size of the area in which ships might stop when ordered to move to the colony; the rate at which pirates passively gain influence when they have ships in the vicinity of a colony appears to be something of the form k + f(FP), where k is a constant offset, FP is the combined firepower of the pirate faction's vessels in the vicinity of the colony, and f(x) appears to be a function whose form is such that the rate at which f(x) grows decreases as x increases); pirate influence is counteracted passively by the colony's population (a colony with a population of around 2-3 billion is more or less immune to passive pirate influence generation, and larger colonies may need to be heavily raided before Hidden Pirate Bases or Fortresses can show up), and the pirate faction controlling a Hidden Pirate Base or Hidden Pirate Fortress is supposed to lose a significant amount of influence when the facility is destroyed. As a result, you may be able to check only a limited number of colonies if you pay attention to where the pirate activity is or to what the colony populations are, and getting Trace Scanners onto your spaceports or other orbital facilities to detect smuggling freighters will reveal the normally-invisible smuggling side of pirate activity.

Trace scanner. That's the ticket. I hadn't realized what that could do for me. And, yes, I have been regularly checking the facilities list on the colonies menu since I got that first alert. Thanks.

Trace scanner. That's the ticket. I hadn't realized what that could do for me.

Trace scanners are for detecting smuggling ships, not pirate facilities.

Thanks again. But let me ask? Could smuggling activity be an indirect indicator of other activity, including a possible pirate base? Or would that be a completely separate thing?

Smuggling ships can generate pirate influence, so at least in theory their presence can give rise to pirate bases, but smuggling ships generate so little influence and generally don't stick around in one place very long, so pirates aren't going to gain enough influence from it to do anything on any colony with more than a very small population. Aside from that, I do not believe that smuggling activity is indicative of other forms of pirate activity.