As a general rule, soldiers are expected to follow the orders of superior officers. However, there are a few special cases to consider. Note that none of these are black and white situations, so there's lots of room for confusion and conflict.

Illegal Orders

Soldiers are expected to refuse illegal orders - i.e. someone ordering them to commit a crime or in some way violate their oath of service.

Example: Captain Smith orders Sergeant Jones to shoot an unarmed civilian. Sergeant Jones refuses.

The trick is whether the soldier can prove that the order was illegal. Things like murder, theft, etc. are probably pretty obvious. But there are gray areas. There was a case in the US Army of a soldier refusing an order to wear UN uniforms because he felt it was illegal. His superior officers disagreed, and he was court-martialed.

Chain of Command

Orders are expected to come through the proper chain of command. It is considered poor form to issue orders to people who do not directly report to you, and may piss off the other person's commander. It is better to talk to the soldier's department head and let THEM issue the order.

Example: Captain Smith (a marine), orders Specialist Jones (a Navy deck hand) to clean the marine bunkroom. Even though Captain Smith outranks Jones, it is not really proper for him to give such an order.

Some exceptions include emergency situations (where typically the highest-ranking officer will assume command and start ordering everybody around), or joint operations (particularly combat), where typically there is a centralized operation commander.
Countermanding Orders

Soldiers are not expected to obey orders that contradict previous orders from a higher-ranking officer.

Example: Colonel Warren ordered Specialist Jones to clean the wardroom. While Jones is cleaning, Captain Smith comes along and orders him to deliver something to CIC. Specialist Jones should continue cleaning the wardroom, because Colonel Warren outranks Captain Smith.

An officer can try to countermand another officer's orders, but this puts both the soldier and the officer in a difficult position. It is better to talk to the superior officer and get him to change his own orders.
Special Authority

Certain positions give special authority to order other people around regardless of rank or department. Some specific examples:

A doctor has jurisdiction over medical stuff. Unlike civilians, military people cannot refuse treatment. If you're ordered to take your vitamins, then by golly you're going to take your vitamins.

Military police have jurisdiction over police matters. An officer could not, for example, order them NOT to arrest someone.

Department heads have jurisdiction over their areas. The engineering chief can order evacuations or order areas sealed off for maintenance; the deck chief can order pilots around if it relates to safety on the deck, etc.

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