I tried to attack the pirates on the ground at one colony but failed multiple times, including when my advisors suggested it. They seem to be extremely entrenched. I am afraid that they will eventually take over all of my colonies? How do I prevent those bases in the first place, and now they're there what's the most effective way to eliminate them? (right now I have troops on auto and have zero experience with ground combat)
Pirates can build pirate bases on your worlds only if they have more than a certain amount of control (which, unfortunately, you can only see as a pirate player; standard empires cannot see this). It's 50% or more control for a Hidden Pirate Base, and I think it might be 100% for a Hidden Pirate Fortress (though I don't remember; it's been a while since I played a pirate empire), and each stage requires the previous facility before it can be constructed. Pirates acquire control of a colony by having ships in orbit (smuggling ships will do, but they don't work particularly well; large groups of warships work better), by raiding a colony (preferably successfully), or by having a station in orbit or in close proximity (say, on the colony's moon), and the rate at which they gain control is dependent on the planet's population, with higher population worlds being more difficult to control. If you can establish control of the local space, pirates cannot gain control of your worlds, though existing bases will prevent control from degrading below a certain level (50% for Hidden Pirate Bases; I forget exactly what for Hidden Pirate Fortresses, and Criminal Networks are special in that they flag the world as belonging to a pirate faction rather than simply allowing the pirates to draw income from it the way the control mechanic does). A colony with a population in excess of ~3 billion or so more or less cannot be controlled by pirates sufficiently for them to build a pirate base upon the surface without extensive raiding, planetary bombardment, or a pre-existing base or fortress, and any world with a population in excess of ~1 billion more or less requires a significant permanent fleet presence or heavy raiding to obtain enough control to build a pirate base upon it. If two or more pirate factions are fighting over a world and neither is really gaining the upper hand permanently, it's possible that neither will be able to hold a planet long enough to establish enough control to build a Hidden Pirate Base/Fortress, and even if they do, there's a possibility for Hidden Pirate Bases and Fortresses to be destroyed by the raids of other pirate factions. Might be a reason to stir up trouble between some pirate factions, if you don't have the fleet forces available to go after them yourself.
5 infantry units is typically adequate to remove a Hidden Pirate Base (though be careful if the pirates have space control, nearby ships with raiders who can be deployed to reinforce the base, or a bonus to ground combat on that planet type). If your troops are among the lower-quality troops (so Atuuk, Teekan, Shandar, Ketarov, Ugnari, Securan, mostly), you might want additional troops or a high population to back them up (Atuuk and Teekan trooops especially; these guys are roughly two thirds as strong as the Shandar, who are the best of the group I've listed and themselves are roughly two-thirds the strength of the best normally recruitable troops (Mortalen, Naxxilian, or Boskaran); as such, with Atuuk or Teekan troops against a completed pirate base, you might want ~10 infantry units. Note that troop strengths are not an empire characteristic but a unit characteristic; an Atuuk empire that recruits Naxxilian troops from a Naxxilian colony it invaded or acquired by some other means will have high-quality Naxxilian troops available, and a Mortalen empire that recruits Teekan troops will have the bad Teekan units rather than its high-quality Mortalen units. Using armor or special forces may help, but that requires research and special recruitment facilities and might require you to shuttle them in on troop transports (which would be at risk if there are pirate ships present); it's probably easier just to locally recruit ~5 infantry units.
I will also add that if you have troops available and you see a pirate facility under construction, it is usually easier to remove the base before it's completed than afterwards. This does depend somewhat on the amount of troops you have immediately available, on their current condition, and on whether or not there are nearby pirates, however.
< Message edited by Aeson -- 5/28/2015 1:29:03 AM >