Reply To: If a captain is incapacitated or killed…
The mission comes first.
On Cook’s third voyage neither HMS Resolution nor HMS Discovery completed the voyage with their original captains. Cook was killed and Clerke died. John Gore (originally 1stLt of Discovery) assumed command of the whole expedition, and it was about a year before the ships returned to UK.
Possibly most extreme example of chain of command was in USS Chesapeake, where William Cox, acting 3rd Lt and senior uninjured officer (though probably unaware of this), effectively became the Captain during the famous battle with HMS Shannon. On return to USA in 1814 he was court-martialled for dereliction of duty and dismissed the service. His descendants fought long to restore his honour, and had the verdict overturned by President Harry Truman 1952