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How should I defend a system against nuisances like pirates? It seems like they swarm me and my fleet sits there picking its nose(on auto). How do I setup defenses that defend?

There is none as far as I can tell. Unless of course you are so technically advanced that your ships totally outmatch the pirates. At that point it becomes easy to auto-defend.

The problem with the AI handling of ships in automation is, that it always tries to go with an appropriate threat-counter. That means, if the pirates show up with a escort-class ship, your automated fleet will activate two of your destroyers or so, thinking that is enough to handle the intruder. While this is true under regular conditions (ships versus ships), it is not appropriate when trying to defend a colony. When the colony is the target of the pirates, it is important that those pirates are taken out as soon as possible. That means they need to be killed before they can launch their assault pods. And that often requires that every ship that is capable of reaching the pirates is beeing thrown at them. By design the AI is not doing that, so... in my experience the only way to have a proper colony defense is to micro for the most part. At least untill you have an overpowered starport or defensive base up... or become so technologically advanced that even the "appropriate" response of the AI has become so powerfull that it vaporizes the pirate within seconds.

The offensive defense strategy, if you have the power: Which pirate faction is attacking? Send an agent there to steal their territory map. Now see their bases, attack and destroy them with your main fleet. They will probably send their ships to defend, destroy them too. After that many years of no disturbance from that faction any more.

I try to set it on patrol on the planet. Seems to work a lot better than telling them to go to a planet and hang around, as all the patrolling ships attack the attacking ships. But they use up fuel to patrol.

ORIGINAL: Plant

I try to set it on patrol on the planet. Seems to work a lot better than telling them to go to a planet and hang around, as all the patrolling ships attack the attacking ships. But they use up fuel to patrol.

A patroling fleet will also only respond with an appropriate force (2 ships per enemy or whatever),... not sure about a bunch of patroling non-fleeted ships. Maybe individual ships will attack all together as each of them considers the threat individually (then patroling or not shouldnt matter). Would have to try that out... but then, I hate unfleeted ships (always messes up the ship list).

Just tested and nope... even individuals are not responding in full force. As far as I can tell there is no way arround microing untill you got a powerfull spaceport or defensive base up.

Well just by taking note of the magnitude of the raids and the tech level, compared to your tech level, is enough to setup a great defense by assigning fleet patrols with the appropriate strength, until you find out their bases and destroy them.

ORIGINAL: xNECROx

How should I defend a system against nuisances like pirates? It seems like they swarm me and my fleet sits there picking its nose(on auto). How do I setup defenses that defend?

Send ground troops with or as soon as you can to any new planet, 3-5 usually enough. This usually stops any pirates who land.
Build refuelling in or as near the system as you can. Resupply vessels are best but gas mining also works but does require extra ships.
Send a fleet (6 DD min) to patrol the system, set posture to defend stance to system.
Build a space port or def base asap, which depends on you needs.
Don't over extend.

Strange. It seems that patrolling planet pirate AI is different from empire planet patrolling.