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Mudassir Ali
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The chain would be determined by seniority of the surface line officers, that is, the officers who are eligible for command. This excludes the staff corps and restricted line officers, such as supply officers, medical officers, or engineering duty officers. On a destroyer, cruiser, or frigate, the only staff corps would be the Supply Officer and the Disbursing Officer. The Disbursing Officer is a junior officer in the Supply Department who deals with the ship’s finances.
So if the Captain is incapacitated, the next in line would be the Executive Officer, followed by the department heads, in order of seniority, then the division officers, in order of seniority. Seniority is determined by year of commissioning. For officers within the same year group, seniority is determined by lineal number, which is a ranking of the line officers Navy-wide.
So if the Captain is incapacitated and there is an Admiral aboard who is staff corps, such as a Medical Officer, command would still go to the Executive Officer, who would be junior to the Admiral.
A Mustang, or Limited Duty Officer, is a former enlisted member who is directly commissioned to work in the area of his enlisted specialty. He has the same rank structure as line officers, but is not eligible for command. Warrant Officers are similar to Limited Duty Officers, but have a different rank structure.
In the case of a catstrophic event in which all line officers are incapacitated, I guess it would go strictly by seniority, including restricted line officers and enlisted.