If we piss a faction off badly enough, they will send their warships looking for us. Our ships are employing cloaking technology, and the hideouts are - well, hidden, but with enough luck and effort they can still be discovered, especially those which are used to launch interceptions. Our enemies are likely to fail and make idiots of themselves anyway, but if they won't, expect them to arrive in a Cruiser, numerous and armed to the teeth. On the bright side, if we kick their asses, their policy is to cover the failure up and they won't return anytime soon. A retaliation is performed by Fighters, Gunships and finally a Cruiser. If any of them manages to get within about 100 miles from our hideout, expect a Cruiser coming fast at it very soon. That last part renders AA defences somewhat impractical, but once the enemy gets boots on the ground, the advantage is ours. The enemy will only be able to deploy in Hangars and the Access Lift.
Special case: the faction is the same as triggered by shooting down a UFO.