New revelations about the National Security Agency’s ability to track phone calls in pre-9/11 America are raising the specter of a massive government cover-up. One that could have been used to hide intelligence failures, and fuel arguments for mass domestic spying.

In 2000, Khalid al-Mihdhar was living in San Diego. One year later, he would go on to be one of the five hijackers aboard American Airlines Flight 77, steered into the Pentagon on September 11. But in the months leading up to that horrifying day, al-Mihdhar made a number of phone calls to Yemen from his California apartment.

Those calls went directly to one of Osama bin Laden’s operation centers in Sanaa, already a major target for US intelligence monitoring.

"One of the 9/11 hijackers, Khalid al-Mihdhar, made a phone call from San Diego to a known al Qaeda safehouse in Yemen," President Obama said during a speech in 2014. "NSA saw that call, but it could not see that the call was coming from an individual already in the United States."

But according to the testimony of agency whistleblowers like Thomas Drake and Kirk Wiebe, it would have been impossible for the agency not to have known the origin of those phone calls.

"You have a target so important to the system that you don’t ever tune a receiver away from that frequency or off of that target," former senior analyst with the NSA Kirk Wiebe told Foreign Policy.

"You know the phone numbers involved, who’s making the phone call, and who it’s going to because the billing system has to have that metadata to charge you."

It’s known as “cast iron” coverage, an intelligence term referring to the 24/7 monitoring of a primary target, like Bin Laden’s Sanaa ops center.

"They’re trying to cover up the failure of the NSA," Wiebe added. "And I think they’re embarrassed by that."

The NSA’s director at the time, Michael Hayden, repeatedly attributed the agency’s failure in anticipating the terrorist attack on weak technical infrastructure. That argument was used to help usher in the Patriot Act, used to justify mass domestic surveillance.

"Nothing in the physics of the intercept, nothing in the content of the call, told us they were in San Diego," Hayden told Frontline last year. "If we’d had the metadata program…those numbers in San Diego would have popped up."

Thomas Drake, a former member of the NSA’s Senior Executive Service, told Foreign Policy that he was shocked by that explanation.

"Not true," Drake said. "That’s an absolute lie. Every number that comes into that switchboard, if you’re cast-iron coverage on that switchboard, you know exactly what that number is and where it comes from…You know exactly – otherwise it can’t get there."

Prior to the Patriot Act, the NSA had any number of ways to access the kind of information Hayden claimed was inaccessible. Through a number of secret agreements with telecommunications satellites, the agency was able to access satellites.

Even those that refused – like Thuraya, which provides mobile coverage to over 160 countries – had their encrypted data routinely breached by the NSA.

"Our secret was that the Thuraya system had been broken for a long time – deep state secret," an anonymous high-ranking source told FP. "Routinely, we could intercept [the satellite transmission] at will. We could take any number that was being dialed in or out…[and] listen in literally live on any conversation or after the fact."

In other words, the NSA had all the technical ability necessary to prevent the 9/11 terrorist attacks long before implementation of the Patriot Act.

While the agency appears to have been covering its own failures, Drake also suggested another reason for the cover up: bureaucratic bickering.

Because of interagency infighting, the NSA refused to share its intelligence with other federal agencies. Michael Scheuer, a former chief with the CIA’s bin Laden desk, made repeated requests for intel to the NSA.

"We sent about 250 electronic messages…and not one of them was ever answered," he told FP.

If the whistleblowers are right, then the September 11 attacks could represent the largest intelligence blunder in history, and the subsequent government cover up may have ushered in the unprecedented domestic spying apparatus employed throughout the last decade.