He was in the nuclear chain of command
When he admitted having an extramarital affair with Paula Broadwell, CIA Director David Petraeus, as a senior civilian in the presidential chain of command should something go catastrophically wrong in Washington, violated special behavior codes for officials who might one day be forced to execute nuclear strikes.
In classified presidential emergency action documents, the CIA director is among the dozens, if not hundreds of officials who are listed as National Command Authority successors in the event that higher ranking officials are no longer able to do their jobs.
Because under certain circumstances he'd have ready access to the nuclear satchel, Petraeus was indoctrinated into the Personnel Reliability Program, which evaluates and monitors the lifestyle and behavior of Americans with access to nuclear command and control mechanisms. Adultery is not a minor sin under the PRP rules.
The details of so-called "nuclear pre-delegation" is one of the most tightly held secrets in the U.S. Government. The first 18 presidential successors are spelled out by law. But it is not clear whether the pre-delegation lists follow the Constitutional chain of command.
After retiring as a general, Petraeus was confirmed by the Senate as a civilian, and was probably given emergency action training by the White House Military Office, which runs the Continuity of Government program. In that role, he could serve as one of the two people needed to confirm codes that would key Permissive Action Links (PALs) and activate launch sequences, adhering to the U.S. Strategic Command's two-person rule for nuclear weapons. Precisely what would need to happen for an official like Petraeus to be in the catbird seat is classified, the result of decades of highly secret rules and provisions that are kept locked in safes.
And so seriously does the U.S. government take the PRP that if a missile wing commander is scheduled to get a wisdom tooth extraction, he or she must notify the squadron's PRP officer, who will transfer power to the deputy commander until the commander's doctor certifies in writing that he or she is able to function normally again.
When Petraeus conceded having an affair to DNI James Clapper, Clapper had several reasons to insist on his resignation, one of which was the director's exalted position in COG programs. Another was simply that the CIA director is held to a higher standard of trust and rectitude by foreign officials, who might take strategic advantage of his public embarrassment.
The current nuclear war plan for the United States is numbered "OPLAN 8010-08" and entitled "Strategic Deference and Global Strike."
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