Need to know: The rarified world of the government’s most closely guarded secrets

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This system of classification is now getting new attention as the Department of Justice investigates whether former President Donald Trump removed classified information from the White House and improperly stored it, including what some officials reportedly worry could be held in special access programs, possibly related to nuclear weapons.

On Friday, the Justice Department released the search warrant that the FBI secured for Trump’s Mar-a-Lago estate, along with a partial description of the items that were seized. They included documents labeled secret, top secret and “TS/SCI,” which stands for top secret/sensitive compartmentalized information, a designation that is also intended to limit distribution.

SAPs can be set up for all types of classified information. “They can be secret or top secret,” said McMillan. “They can be all flavors.”

Officially, a SAP is defined by executive order as “a program established for a specific class of classified information that imposes safeguarding and access requirements that exceed those normally required for information at the same classification level.”

A former senior intelligence official described the network of SAPs as “its own ecosystem in the biodome of classified programs.”

The official, who agreed to speak about the sensitive topic on condition of anonymity, offered an analogy: If a building contained classified information, many officials would have access to the facility. But the SAPs would be locked in a single room with only a handful of personnel provided keys — and only because they need the information to carry out their specific duties.

SAPs, which at the Pentagon can be approved only by the secretary or deputy secretary of Defense, cover a range of subjects.

That can include intelligence, along with the sources for the information, collected from spies overseas, or details about the technical means to gather intelligence, such as from satellites or eavesdropping devices. Many other SAPs shield data on specific weapon systems in the American arsenal or the military capabilities of foreign adversaries.

“Sometimes it’s a vulnerability, something that has a limitation: it doesn’t do ‘x,’” explained a former senior intelligence official with access to a number of SAPs who also asked to not be identified discussing internal procedures. “Sometimes it’s something really, really cool that we don’t want the adversary to develop a defense against.”

“You have access to it because essentially you are put on a list and the only people who can access that category of information are people who are on that list,” the former official added.

Some special access programs also contain multiple layers that could each have different levels of classification.

Experts say the vast majority are “acquisition SAPs” involving highly technical information about weapons systems that are under development or have advanced capabilities.

McMillan said the Center for Development of Security Excellence, which trains Pentagon officials and contractors on the handling of classified information, estimates that up to 80 percent of Pentagon SAPs involve acquisition programs.

One recent example is the Air Force’s nuclear-armed B-21 stealth bomber that is being developed by Northrop Grumman. It is designated a SAP due to the sensitivity of the technologies.

But that is an “acknowledged SAP.” While the Air Force doesn’t divulge details of the program itself, it is publicly known that the project falls in a special category to protect it from prying eyes or ears.

Then there are also “unacknowledged” SAPs, for which funding is purposely hidden in the federal budget and their existence is denied to those who are not cleared.

The Center for Development of Security Excellence describes them as SAPs “whose existence and purpose are protected” and “program funding for unacknowledged SAPs is often classified, unacknowledged, or not directly linked to the program.”

Even the highest level of officials who have access to the most sensitive intelligence aren’t necessarily read in on all SAPs.

“There are a small number of people who are so-called ‘super users’ who have access to any SAP,” said Eric Edelman, who served as undersecretary of Defense for policy in the administration of George W. Bush and as ambassador to Turkey and Finland. “I was technically a super user as undersecretary, but was I read into every SAP? Hell no. I didn’t necessarily need to know about a lot of the things. If I needed to, I would be brought into whatever it was.”

But the White House, he said, would have some of the broadest access into this netherworld of American secrets.

“At the White House, everything sort of kind of flows into that because you’ve got oversight of all the departments,” Edelman said.

And Trump was known to widely disrespect classification rules.

“If a general came to him and briefed him on something, ‘Mr. President, this is really, really important, it absolutely can’t get out to enemies,’ he might have taken that with a grain of salt,” recalled the former senior intelligence official, who briefed him on numerous occasions.

Trump often appeared unconvinced and expressed the view that “these damn generals are so damn cautious. They don’t know how to win a war anymore. I know better,” the former senior official said.

Trump and his allies contend that anything seized at his Florida resort was declassified under his authority as president.

Even if that were true, “that doesn’t mean that he has the right to physically take it when he’s no longer president,” said Edelman.

If Trump is charged and found guilty of removing the classified documents without the proper authorization, he could face up to five years in prison under federal law — a punishment that was extended from one year during Trump’s first year in office.

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