First of all, I recommend you post in the Sins of a Solar Empire forums somewhere. For this probably the main forum will do. Some forums like this one (Stardockians) and say PC Gaming or Off Topic are shared between all Stardock forums, so people say browsing the Galactic Civilizations forums might see this and give you answers for the totally wrong game (or just be confused).
Anyway, military victory is the default victory option. Technically it occurs when all of your enemies have lost yet none of the other victory conditions have been triggered. Strictly speaking without other victory conditions in play, this means that you have destroyed all of your enemies' planets (or if the Vasari Loyalists got far enough in the game to research a certain tech, you need to destroy their titan, capitalships and starbases too).
However, it is also possible for enemies, including the AI, to surrender before losing all their planets, so it can seem rather unexpected when it comes. But you can always trigger a military victory by taking all your enemies planets, if your last enemy surrenders you'll just get the victory earlier, since there are no more enemy players to play against.