Complex sentence: The commander of Dancon is usually the commander of the hierarchically biggest military unit associated with the specified mission, and does not have a headquarters of its own, but rather it is that military unit's headquarters.
Split into simpler sentences: The commander of Dancon is usually the commander of the hierarchically biggest military unit associated with the specified mission. And as such "Dancon" does not have a headquarters of its own, but rather it is that military unit's headquarters.