Nearly two years before 9/11, America's largest intelligence agency had recordings of three of the al Qaeda hijackers plotting an attack. But the information, obtained by the National Security Agency, wasn't analyzed in a way that could uncover the plot.

Inside the super-secret NSA, several analysts and managers believed the agency had a powerful tool that might have had a chance to head off 9/11. But it wasn't used.

One of those agency insiders was Thomas Drake, who thought taxpayer money was being wasted on useless intelligence gathering projects while promising technology was ignored.

Drake tried to get the word out. But now, as a result, he has been charged under the Espionage Act of 1917 and if convicted of all charges could spend the next 35 years of his life in prison. The government says he betrayed his country.

Drake says the only thing he betrayed was NSA mismanagement that undermined national security.

After a long career in U.S. intelligence, Drake never imagined he'd be labeled an enemy of the United States. As a young airman, he flew spy missions in the Cold War; in the Navy, he analyzed intelligence for the joint chiefs at the Pentagon.

Later, he worked for defense contractors in the highly technical world of electronic eavesdropping. He became an expert in sophisticated, top secret computer software programs and ultimately rose, in 2001, to a senior executive job at the NSA.

Drake told correspondent Scott Pelley his first day on the job was Sept. 11, 2001.

"NSA went into immediate crisis management mode. We had failed to protect the United States of America," he told Pelley.

Asked if he felt that was a failure of the NSA, Drake told Pelley, "The entire national security establishment - it was a failure, a fundamental systemic breakdown."

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Part of the failure at the NSA, the largest U.S. intelligence agency, was in its old technology. The agency eavesdrops on the communications of the world. But in the 1990s it was becoming ineffective, overwhelmed by the explosion of digital data.

"Vast volumes of data streaming across all kinds of different networks, wired, wireless, phones, computers, you name it," Drake explained.

"And what does that look like to NSA? Coming into building in Maryland?" Pelley asked.

"Choking on it," Drake said. "Just incredible amounts. Even just storing it was becoming a challenge."

Most of what the agency collected went unanalyzed, including clues pointing to 9/11. Kirk Wiebe and Bill Binney were career NSA intelligence analysts who were working on the problem.

"We were greatly saddened and shocked by 9/11, but it didn't come as a total surprise. We knew there was a vulnerability, a lack of understanding of the data that put NSA in a weak position," Wiebe said.

Recognizing that vulnerability in the late 1990s, Binney, a legendary NSA mathematician, led development of a revolutionary computer system to collect, isolate and connect important information like phone calls and financial transactions. Its code name was "Thin Thread."

"Thin Thread was fundamentally dedicated to collecting and processing and ultimately analyzing the vast reams of digital data. It was a breakthrough solution," Drake explained.

Produced Glenn Silber and Graham Messick