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I was relieved to have one of al Qaeda’s senior leaders off the battlefield. But my relief did not last long. Agents searching Khalid Sheikh Mohammed’s compound discovered what one official later called a “mother lode” of valuable intelligence. Khalid Sheikh Mohammed was obviously planning more attacks. It didn’t sound like he was willing to give us any information about them. “I’ll talk to you,” he said, “after I get to New York and see my lawyer.”

George Tenet asked if he had permission to use enhanced interrogation techniques, including waterboarding, on Khalid Sheikh Mohammed. I thought about my meeting with Danny Pearl’s widow, who was pregnant with his son when he was murdered. I thought about the 2,973 people stolen from their families by al Qaeda on 9/11. And I thought about my duty to protect the country from another act of terror.

“Damn right,” I said.

Khalid Sheikh Mohammed proved difficult to break. But when he did, he gave us a lot. He disclosed plans to attack American targets with anthrax and directed us to three people involved in the al Qaeda biological weapons program. He provided information that led to the capture of Hambali, the chief of al Qaeda’s most dangerous affiliate in Southeast Asia and the architect of the Bali terrorist attack that killed 202 people. He provided further details that led agents to Hambali’s brother, who had been grooming operatives to carry out another attack inside the United States, possibly a West Coast version of 9/11 in which terrorists flew a hijacked plane into the Library Tower in Los Angeles.

Years later, the Washington Post ran a front-page story about Khalid Sheikh Mohammed’s transformation. Headlined “How a Detainee Became an Asset,” it described how Mohammed “seemed to relish the opportunity, sometimes for hours on end, to discuss the inner workings of al-Qaeda and the group’s plans, ideology and operatives. … He’d even use a chalkboard at times.” The intelligence he provided, which proved vital to saving American lives, almost certainly would not have come to light without the CIA’s enhanced interrogation program.

Of the thousands of terrorists we captured in the years after 9/11, about a hundred were placed into the CIA program. About a third of those were questioned using enhanced techniques. Three were waterboarded. The information the detainees in the CIA program revealed constituted more than half of what the CIA knew about al Qaeda. Their interrogations helped break up plots to attack American military and diplomatic facilities abroad, Heathrow Airport and Canary Wharf in London, and multiple targets in the United States. Experts in the intelligence community told me that without the CIA program, there would have been another attack on the United States.

After we implemented the CIA program, we briefed a small number of lawmakers from both parties on its existence. At the time, some were concerned we weren’t pushing hard enough. But years later, once the threat seemed less urgent and the political winds had shifted, many lawmakers became fierce critics. They charged that Americans had committed unlawful torture. That was not true. I had asked the most senior legal officers in the U.S. government to review the interrogation methods, and they had assured me they did not constitute torture. To suggest that our intelligence personnel violated the law by following the legal guidance they received is insulting and wrong.

The CIA interrogation program saved lives. Had we captured more al Qaeda operatives with significant intelligence value, I would have used the program for them as well.

On the morning of March 10, 2004, Dick Cheney and Andy Card greeted me with a startling announcement: The Terrorist Surveillance Program would expire at the end of the day.

“How can it possibly end?” I asked. “It’s vital to protecting the country.” Two and a half years had passed since I authorized the TSP in October 2001. In that time, the NSA had used the program to uncover key details about terrorist plots and locations. NSA Director Mike Hayden later said publicly that the program had been “successful in detecting and preventing attacks inside the United States” and that it was his “professional judgment that we would have detected some of the 9/11 al Qaeda operatives in the United States” if it had been operational before the attacks.

Andy explained the situation. While John Ashcroft had regularly recommended the renewal of the TSP since 2001, the Justice Department had raised a legal objection to one component of the program.

“Why didn’t I know about this?” I asked. Andy shared my disbelief. He told me he had just learned about the objection the previous night. The legal team must have thought the disagreement could be settled without presidential involvement. I told Andy to work with Ashcroft and White House Counsel Alberto Gonzales to solve the problem. In the meantime, I had to fly to Cleveland to deliver a speech on trade policy.

When I got back, I checked in with Andy. Little progress had been made. The Justice Department was sticking to its objection. My lawyers weren’t budging, either. They were convinced the program was legal.

“Where the hell is Ashcroft?” I asked.

“He’s in the hospital,” Andy replied.

That was news to me. I called John, who I discovered was recovering from emergency gallbladder surgery. I told him I was sending Andy and Al to talk to him about an urgent matter. They drove to the hospital with the TSP reauthorization order. When they got back, they told me Ashcroft hadn’t signed. The only way to allow the program to continue was to override the Justice Department’s objection. I didn’t like the idea, but I saw no other alternative. I signed an order keeping the TSP alive based on my authority as head of the executive branch.

I went to bed irritated and had a feeling I didn’t know the full story. I intended to get it.

“Mr. President, we’ve got a major problem,” Andy told me when I got to the Oval Office on the morning of March 12. “Jim Comey is the acting attorney general, and he’s going to resign because you extended the TSP. So are a bunch of other Justice Department officials.”

I was stunned. Nobody had told me that Comey, John Ashcroft’s deputy, had taken over Ashcroft’s responsibilities when he went in for surgery. If I had known that, I never would have sent Andy and Al to John’s hospital room.

I asked to speak to Comey privately after the morning FBI briefing, which he attended in John Ashcroft’s place. I hadn’t spent a lot of time with Jim, but I knew he had a distinguished record as a prosecutor in New York. I started by explaining that I had an obligation to do what was necessary to protect the country. I felt the TSP was essential to that effort. He explained his concerns about the problematic aspect of the program. “I just don’t understand why you are raising this at the last minute,” I said.

He looked shocked. “Mr. President,” he said, “your staff has known about this for weeks.” Then he dropped another bomb. He wasn’t the only one planning to resign. So was FBI Director Bob Mueller. I was about to witness the largest mass resignation in modern presidential history, and we were in the middle of a war.

I called Bob into the Oval Office. I had come to know him well over the past two and a half years. He was a good and decent man, a former Princeton hockey star who had served in the Marines and led the U.S. Attorney’s Office in San Francisco. Without hesitation, he agreed with Comey. If I continued the program over the Justice Department’s objection, he said, he couldn’t serve in my administration.

I had to make a big decision, and fast. Some in the White House believed I should stand on my powers under Article II of the Constitution and suffer the walkout. Others counseled that I accept Justice’s objections, modify the program, and keep the administration intact.

I was willing to defend the powers of the presidency under Article II. But not at any cost. I thought about the Saturday Night Massacre in October 1973, when President Richard Nixon’s firing of Watergate prosecutor Archibald Cox led his attorney general and deputy attorney general to resign. That was not a historical crisis I was eager to replicate. It wouldn’t give me much satisfaction to know I was right on the legal principles while my administration imploded and our key programs in the war on terror were exposed in the media firestorm that would inevitably follow.

I decided to accommodate the Justice Department’s concern by modifying the part of the program they found problematic, while leaving the TSP in place. Comey and Mueller dropped their resignation threats. The surveillance program continued to produce results, and that was the most important thing.

I was relieved to have the crisis over, but I was disturbed it had happened at all. I made clear to my advisers that I never wanted to be blindsided like that again. I did not suspect bad intentions on anyone’s part. One of the toughest questions every White House faces is how to manage the president’s time and when to bring policy disputes to his desk. The standoff over the surveillance program was a case of bad judgment. There was no shortage of disagreements in the years ahead, but nothing like this ever happened again.