Yeah, I mentioned the letters of last resort, but while the letter will contain orders, the captain has sole launch authority, and it's difficult to imagine the system could work in a way that avoids that - whatever process you require the captain to follow, they could simply decide to follow that process as though the leadership were uncontactable.
I don't know what the actual procedure is; however like with Science Fiction and 'Self Destruct' codes I would think that a multi-agent auth challenge would be required.
The captain and some fixed number of executive officers. Possibly with redundancy for one or two crew being dead. The auth codes would cause a safe to unlock or message to de-crypt.
Presumably the instructions would be delivered to each authenticating member so that all could receive the orders simultaneously.
