On June 13th, a fifty-four-year-old former government employee named Thomas Drake is scheduled to appear in a courtroom in Baltimore, where he will face some of the gravest charges that can be brought against an American citizen. A former senior executive at the National Security Agency, the government’s electronic-espionage service, he is accused, in essence, of being an enemy of the state. According to a ten-count indictment delivered against him in April, 2010, Drake violated the Espionage Act—the 1917 statute that was used to convict Aldrich Ames, the C.I.A. officer who, in the eighties and nineties, sold U.S. intelligence to the K.G.B., enabling the Kremlin to assassinate informants. In 2007, the indictment says, Drake willfully retained top-secret defense documents that he had sworn an oath to protect, sneaking them out of the intelligence agency’s headquarters, at Fort Meade, Maryland, and taking them home, for the purpose of “unauthorized disclosure.” The aim of this scheme, the indictment says, was to leak government secrets to an unnamed newspaper reporter, who is identifiable as Siobhan Gorman, of the Baltimore Sun. Gorman wrote a prize-winning series of articles for the Sun about financial waste, bureaucratic dysfunction, and dubious legal practices in N.S.A. counterterrorism programs. Drake is also charged with obstructing justice and lying to federal law-enforcement agents. If he is convicted on all counts, he could receive a prison term of thirty-five years.

The government argues that Drake recklessly endangered the lives of American servicemen. “This is not an issue of benign documents,” William M. Welch II, the senior litigation counsel who is prosecuting the case, argued at a hearing in March, 2010. The N.S.A., he went on, collects “intelligence for the soldier in the field. So when individuals go out and they harm that ability, our intelligence goes dark and our soldier in the field gets harmed.”

Top officials at the Justice Department describe such leak prosecutions as almost obligatory. Lanny Breuer, the Assistant Attorney General who supervises the department’s criminal division, told me, “You don’t get to break the law and disclose classified information just because you want to.” He added, “Politics should play no role in it whatsoever.”

When President Barack Obama took office, in 2009, he championed the cause of government transparency, and spoke admiringly of whistle-blowers, whom he described as “often the best source of information about waste, fraud, and abuse in government.” But the Obama Administration has pursued leak prosecutions with a surprising relentlessness. Including the Drake case, it has been using the Espionage Act to press criminal charges in five alleged instances of national-security leaks—more such prosecutions than have occurred in all previous Administrations combined. The Drake case is one of two that Obama’s Justice Department has carried over from the Bush years.

Gabriel Schoenfeld, a conservative political scientist at the Hudson Institute, who, in his book “Necessary Secrets” (2010), argues for more stringent protection of classified information, says, “Ironically, Obama has presided over the most draconian crackdown on leaks in our history—even more so than Nixon.”

One afternoon in January, Drake met with me, giving his first public interview about this case. He is tall, with thinning sandy hair framing a domed forehead, and he has the erect bearing of a member of the Air Force, where he served before joining the N.S.A., in 2001. Obsessive, dramatic, and emotional, he has an unwavering belief in his own rectitude. Sitting at a Formica table at the Tastee Diner, in Bethesda, Drake—who is a registered Republican—groaned and thrust his head into his hands. “I actually had hopes for Obama,” he said. He had not only expected the President to roll back the prosecutions launched by the Bush Administration; he had thought that Bush Administration officials would be investigated for overstepping the law in the “war on terror.”

“But power is incredibly destructive,” Drake said. “It’s a weird, pathological thing. I also think the intelligence community coöpted Obama, because he’s rather naïve about national security. He’s accepted the fear and secrecy. We’re in a scary space in this country.”

The Justice Department’s indictment narrows the frame around Drake’s actions, focussing almost exclusively on his handling of what it claims are five classified documents. But Drake sees his story as a larger tale of political reprisal, one that he fears the government will never allow him to air fully in court. “I’m a target,” he said. “I’ve got a bull’s-eye on my back.” He continued, “I did not tell secrets. I am facing prison for having raised an alarm, period. I went to a reporter with a few key things: fraud, waste, and abuse, and the fact that there were legal alternatives to the Bush Administration’s ‘dark side’ ”—in particular, warrantless domestic spying by the N.S.A.

The indictment portrays him not as a hero but as a treacherous man who violated “the government trust.” Drake said of the prosecutors, “They can say what they want. But the F.B.I. can find something on anyone.”

Steven Aftergood, the director of the Project on Government Secrecy at the Federation of American Scientists, says of the Drake case, “The government wants this to be about unlawfully retained information. The defense, meanwhile, is painting a picture of a public-interested whistle-blower who struggled to bring attention to what he saw as multibillion-dollar mismanagement.” Because Drake is not a spy, Aftergood says, the case will “test whether intelligence officers can be convicted of violating the Espionage Act even if their intent is pure.” He believes that the trial may also test whether the nation’s expanding secret intelligence bureaucracy is beyond meaningful accountability. “It’s a much larger debate than whether a piece of paper was at a certain place at a certain time,” he says.

Jack Balkin, a liberal law professor at Yale, agrees that the increase in leak prosecutions is part of a larger transformation. “We are witnessing the bipartisan normalization and legitimization of a national-surveillance state,” he says. In his view, zealous leak prosecutions are consonant with other political shifts since 9/11: the emergence of a vast new security bureaucracy, in which at least two and a half million people hold confidential, secret, or top-secret clearances; huge expenditures on electronic monitoring, along with a reinterpretation of the law in order to sanction it; and corporate partnerships with the government that have transformed the counterterrorism industry into a powerful lobbying force. Obama, Balkin says, has “systematically adopted policies consistent with the second term of the Bush Administration.”

On March 28th, Obama held a meeting in the White House with five advocates for greater transparency in government. During the discussion, the President drew a sharp distinction between whistle-blowers who exclusively reveal wrongdoing and those who jeopardize national security. The importance of maintaining secrecy about the impending raid on Osama bin Laden’s compound was likely on Obama’s mind. The White House has been particularly bedevilled by the ongoing release of classified documents by WikiLeaks, the group led by Julian Assange. Last year, WikiLeaks began releasing a vast trove of sensitive government documents allegedly leaked by a U.S. soldier, Bradley Manning; the documents included references to a courier for bin Laden who had moved his family to Abbottabad—the town where bin Laden was hiding out. Manning has been charged with “aiding the enemy.”

Danielle Brian, the executive director of the Project on Government Oversight, attended the meeting, and said that Obama’s tone was generally supportive of transparency. But when the subject of national-security leaks came up, Brian said, “the President shifted in his seat and leaned forward. He said this may be where we have some differences. He said he doesn’t want to protect the people who leak to the media war plans that could impact the troops.” Though Brian was impressed with Obama’s over-all stance on transparency, she felt that he might be misinformed about some of the current leak cases. She warned Obama that prosecuting whistle-blowers would undermine his legacy. Brian had been told by the White House to avoid any “ask”s on specific issues, but she told the President that, according to his own logic, Drake was exactly the kind of whistle-blower who deserved protection.

As Drake tells it, his problems began on September 11, 2001. “The next seven weeks were crucial,” he said. “It’s foundational to why I am a criminal defendant today.”

The morning that Al Qaeda attacked the U.S. was, coincidentally, Drake’s first full day of work as a civilian employee at the N.S.A.—an agency that James Bamford, the author of “The Shadow Factory” (2008), calls “the largest, most costly, and most technologically sophisticated spy organization the world has ever known.” Drake, a linguist and a computer expert with a background in military crypto-electronics, had worked for twelve years as an outside contractor at the N.S.A. Under a program code-named Jackpot, he focussed on finding and fixing weaknesses in the agency’s software programs. But, after going through interviews and background checks, he began working full time for Maureen Baginski, the chief of the Signals Intelligence Directorate at the N.S.A., and the agency’s third-highest-ranking official.

Even in an age in which computerized feats are commonplace, the N.S.A.’s capabilities are breathtaking. The agency reportedly has the capacity to intercept and download, every six hours, electronic communications equivalent to the contents of the Library of Congress. Three times the size of the C.I.A., and with a third of the U.S.’s entire intelligence budget, the N.S.A. has a five-thousand-acre campus at Fort Meade protected by iris scanners and facial-recognition devices. The electric bill there is said to surpass seventy million dollars a year.

Nevertheless, when Drake took up his post the agency was undergoing an identity crisis. With the Cold War over, the agency’s mission was no longer clear. As Drake puts it, “Without the Soviet Union, it didn’t know what to do.” Moreover, its technology had failed to keep pace with the shift in communications to cellular phones, fibre-optic cable, and the Internet. Two assessments commissioned by General Michael Hayden, who took over the agency in 1999, had drawn devastating conclusions. One described the N.S.A. as “an agency mired in bureaucratic conflict” and “suffering from poor leadership.” In January, 2000, the agency’s computer system crashed for three and a half days, causing a virtual intelligence blackout.

Agency leaders decided to “stir up the gene pool,” Drake says. Although his hiring was meant to signal fresh thinking, he was given a clumsy bureaucratic title: Senior Change Leader/Chief, Change Leadership & Communications Office, Signals Intelligence Directorate.

The 9/11 attacks caught the U.S.’s national-security apparatus by surprise. N.S.A. officials were humiliated to learn that the Al Qaeda hijackers had spent their final days, undetected, in a motel in Laurel, Maryland—a few miles outside the N.S.A.’s fortified gates. They had bought a folding knife at a Target on Fort Meade Road. Only after the attacks did agency officials notice that, on September 10th, their surveillance systems had intercepted conversations in Afghanistan and Saudi Arabia warning that “the match begins tomorrow” and “tomorrow is Zero Hour.”

Drake, hoping to help fight back against Al Qaeda, immediately thought of a tantalizing secret project he had come across while working on Jackpot. Code-named ThinThread, it had been developed by technological wizards in a kind of Skunk Works on the N.S.A. campus. Formally, the project was supervised by the agency’s Signals Intelligence Automation Research Center, or SARC.

While most of the N.S.A. was reeling on September 11th, inside SARC the horror unfolded “almost like an ‘I-told-you-so’ moment,” according to J. Kirk Wiebe, an intelligence analyst who worked there. “We knew we weren’t keeping up.” SARC was led by a crypto-mathematician named Bill Binney, whom Wiebe describes as “one of the best analysts in history.” Binney and a team of some twenty others believed that they had pinpointed the N.S.A.’s biggest problem—data overload—and then solved it. But the agency’s management hadn’t agreed.

Binney, who is six feet three, is a bespectacled sixty-seven-year-old man with wisps of dark hair; he has the quiet, tense air of a preoccupied intellectual. Now retired and suffering gravely from diabetes, which has already claimed his left leg, he agreed recently to speak publicly for the first time about the Drake case. When we met, at a restaurant near N.S.A. headquarters, he leaned crutches against an extra chair. “This is too serious not to talk about,” he said.

Binney expressed terrible remorse over the way some of his algorithms were used after 9/11. ThinThread, the “little program” that he invented to track enemies outside the U.S., “got twisted,” and was used for both foreign and domestic spying: “I should apologize to the American people. It’s violated everyone’s rights. It can be used to eavesdrop on the whole world.” According to Binney, Drake took his side against the N.S.A.’s management and, as a result, became a political target within the agency.

Binney spent most of his career at the agency. In 1997, he became the technical director of the World Geopolitical and Military Analysis Reporting Group, a division of six thousand employees which focusses on analyzing signals intelligence. By the late nineties, the N.S.A. had become overwhelmed by the amount of digital data it was collecting. Binney and his team began developing codes aimed at streamlining the process, allowing the agency to isolate useful intelligence. This was the beginning of ThinThread.

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In the late nineties, Binney estimated that there were some two and a half billion phones in the world and one and a half billion I.P. addresses. Approximately twenty terabytes of unique information passed around the world every minute. Binney started assembling a system that could trap and map all of it. “I wanted to graph the world,” Binney said. “People said, ‘You can’t do this—the possibilities are infinite.’ ” But he argued that “at any given point in time the number of atoms in the universe is big, but it’s finite.”

As Binney imagined it, ThinThread would correlate data from financial transactions, travel records, Web searches, G.P.S. equipment, and any other “attributes” that an analyst might find useful in pinpointing “the bad guys.” By 2000, Binney, using fibre optics, had set up a computer network that could chart relationships among people in real time. It also turned the N.S.A.’s data-collection paradigm upside down. Instead of vacuuming up information around the world and then sending it all back to headquarters for analysis, ThinThread processed information as it was collected—discarding useless information on the spot and avoiding the overload problem that plagued centralized systems. Binney says, “The beauty of it is that it was open-ended, so it could keep expanding.”