Shortly after 9:30 p.m., President Bush brought together his most senior national security advisers in a bunker beneath the White House grounds. It was just 13 hours after the deadliest attack on the U.S. homeland in the country's history...

"This is the time for self-defense," he told his aides, according to National Security Council notes. Then, repeating the vow he had made earlier in the evening in a televised address from the Oval Office, he added: "We have made the decision to punish whoever harbors terrorists, not just the perpetrators."

Their job, the president said, was to figure out how to do it.

That afternoon, on a secure phone on Air Force One, Bush had already told Defense Secretary Donald H. Rumsfeld that he would order a military response and that Rumsfeld would be responsible for organizing it. "We'll clean up the mess," the president told Rumsfeld, "and then the ball will be in your court."

Intelligence was by now almost conclusive that Osama bin Laden and his al Qaeda network, based in Afghanistan, had carried out the attacks on the World Trade Center and the Pentagon. But the aides gathered in the bunker-the "war cabinet" that included Rumsfeld, Vice President Cheney, national security adviser Condoleezza Rice, Secretary of State Colin L. Powell and CIA Director George J. Tenet-were not ready to say what should be done about them. The war cabinet had questions, no one more than Rumsfeld.

Who are the targets? How much evidence do we need before going after al Qaeda? How soon do we act? While acting quickly was essential, Rumsfeld said, it might take up to 60 days to prepare for major military strikes. And, he asked, are there targets that are off-limits? Do we include American allies in military strikes?

Rumsfeld warned that an effective response would require a wider war, one that went far beyond the use of military force. The United States, he said, must employ every tool available-military, legal, financial, diplomatic, intelligence.

The president was enthusiastic. But Tenet offered a sobering thought. Although al Qaeda's home base was Afghanistan, the terrorist organization operated nearly worldwide, he said. The CIA had been working the bin Laden problem for years. We have a 60-country problem, he told the group.

"Let's pick them off one at a time," Bush replied

After the president returned to the White House on Sept. 11, he and his top advisers, including Clarke, began holding meetings about how to respond and retaliate. As Clarke writes in his book, he expected the administration to focus its military response on Osama bin Laden and al Qaeda. He says he was surprised that the talk quickly turned to Iraq.

"Rumsfeld was saying that we needed to bomb Iraq," Clarke said to Stahl. "And we all said ... no, no. Al-Qaeda is in Afghanistan. We need to bomb Afghanistan. And Rumsfeld said there aren't any good targets in Afghanistan. And there are lots of good targets in Iraq. I said, 'Well, there are lots of good targets in lots of places, but Iraq had nothing to do with it.

"Initially, I thought when he said, 'There aren't enough targets in-- in Afghanistan,' I thought he was joking.

"I think they wanted to believe that there was a connection, but the CIA was sitting there, the FBI was sitting there, I was sitting there saying we've looked at this issue for years. For years we've looked and there's just no connection."

Clarke says he and CIA Director George Tenet told that to Rumsfeld, Secretary of State Colin Powell, and Attorney General John Ashcroft.

Clarke then tells Stahl of being pressured by Mr. Bush.

"The president dragged me into a room with a couple of other people, shut the door, and said, 'I want you to find whether Iraq did this.' Now he never said, 'Make it up.' But the entire conversation left me in absolutely no doubt that George Bush wanted me to come back with a report that said Iraq did this.

"I said, 'Mr. President. We've done this before. We have been looking at this. We looked at it with an open mind. There's no connection.'

"He came back at me and said, "Iraq! Saddam! Find out if there's a connection.' And in a very intimidating way. I mean that we should come back with that answer. We wrote a report."

"Iraq, as the president has said, is at the center of the war on terror. We have narrowed the ground available to al Qaeda and to the terrorists. Their sanctuary in Afghanistan is gone; their sanctuary in Iraq is gone. Saudi Arabia and Pakistan are now allies on the war on terror. So Iraq has contributed in that way in narrowing the sanctuaries available to terrorists."

Allah has granted the Muslim people and the Afghani mujahedeen, and those with them, the opportunity to fight the Russians and the Soviet Union. ... They were defeated by Allah and were wiped out. There is a lesson here. The Soviet Union entered Afghanistan late in December of '79. The flag of the Soviet Union was folded once and for all on the 25th of December just 10 years later. It was thrown in the waste basket. Gone was the Soviet union forever.

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Today however, our battle against the Americans is far greater than our battle was against the Russians. Americans have committed unprecedented stupidity. They have attacked Islam and its most significant sacrosanct symbols ... . We anticipate a black future for America. Instead of remaining United States, it shall end up separated states and shall have to carry the bodies of its sons back to America.