It would depend on the navy your writing about for example the procedure on crimson time is fairly accurate for the USN but its a completely different procedure for the Royal Navy.
The RN doesn't use the PAL codes although some elements of the USN procedures are present such as "set condition 1SQ" (depending on launch type will depend on what comes next).
Theres a set routine including coming to depth and commencing hovering, the call to action stations missile and a procedure to check the letter of last resort ect.
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