In each battle there is a Chain of Command for each side. At the top of the Chain of Command is the Commander in Chief (Cic). Each side must have a Cic, no matter what his rank is. He is usually the most superior officer (but not always).

For example, in most large battles he will be an Army Commander (4 stars). The rank of a commander is independent of whether they are the Cic or not. For example, if you play Pickett's Charge, Hancock, the 2nd Corps Commander, is the Cic purely for game play. Because he is Cic, the orders come down from him to Newton, the Corps Commander of 1st Corps. However, this is historically not correct but for game play it makes sense to organize the units this way. Under the Cic are the other subordinate commanders. The chain of command flows from the Cic, to subordinate commanders, to their subordinate commander, etc., until the chain of command reaches the brigades.

Brigades and batteries are usually under the control of a Divisional commander. However, sometimes independent brigades may be under the direct control of a Corps commander, and sometimes even an army commander. This is very important when considering who a brigade or battery is receiving its orders from (see command distance).

Sometime throughout the course of a battle a Commander may be killed or wounded. The commander does not have to be physically involved in a fight but merely within 3 hexes of any fighting. There is a small chance they will be a casualty (due to flying shrapnel or sharpshooters). If they do become a casualty, it takes one turn for a replacement to be appointed.

During this time the command distance of the commander unit is reduced to zero (see command distance).

If the commander who was killed was an Exceptional commander, the replacement will not be exceptional.