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For most military matters, Congress has the final say. The president does have executive order over some things, and there are certain ways that the president can get around the power of congress in some matters.
It depends which country you are referring to.
Paternalistic
Federalism in America allows for the Supreme Court which is the highest authority in the union to have final decision matters over individual states.
The final authority over what? The answer to this question depends on the subject under discussion.
Who was banished from the Massachusetts Bay Colony because he was a Separatist who believed that the government had no authority over religious matters.
A caesaropapism is a doctrine that the state has authority over the church in ecclesiastical matters.
when military authority takes priority over an event on a military installion or an offense by a member of the military
Who had the final authority over the colonists, royal governors, colonial legislatures, citizens themselves, the English monarch
your family
hell no
As the Commander in Chief the US President has authority over the entire military, so all of them. He has the authority to deploy up to 400,000 at a time without needing the approval of Congress