Nuclear launch orders come from POTUS and Verified by Secretary of Defense.
Further down the line the 2 man rule is in effect but in the field, there is no way to know if those have been compromised, commanders would launch a missile because the codes would verify.
We have seen in books and movies this play out (Sum of All Fears, Crimson Tide) where the order was refused by humans still in some control and Wargames where a computer took this out of the hands of people.