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As evidence of al Qaeda's responsibility for the Cole attack came in during November 2000, National Security Advisor Samuel Berger asked the Pentagon to develop a plan for a sustained air campaign against the Taliban. Clarke developed a paper laying out a formal, specific ultimatum. But Clarke's plan apparently did not advance to formal consideration by the Small Group of principals. We have found no indication that the idea was briefed to the new administration or that Clarke passed his paper to them, although the same team of career officials spanned both administrations.

After the October 2000 attack on the USS Cole, evidence accumulated that it had been launched by al Qaeda operatives, but without confirmation that Bin Ladin had given the order. The Taliban had earlier been warned that it would be held responsible for another Bin Ladin attack on the United States. The CIA described its findings as a "preliminary judgment"; President Clinton and his chief advisers told us they were waiting for a conclusion before deciding whether to take military action. The military alternatives remained unappealing to them.

Clinton says this...

"I desperately wish, that I had been president when the FBI and CIA finally confirmed, officially, that bin Laden was responsible for the attack on the U.S.S. Cole. Then we could have launched an attack on Afghanistan early."

In 1998, we learned that Osama bin Laden's organization Al Qaeda was responsible for acts of terrorism against the United States, eventually including "the 1993 World Trade Center bombing, the 1996 killing of 19 US soldiers in Saudi Arabia, and the 1998 bombings in Kenya and Tanzania". In 1999, he was added to the FBI's 10 Most Wanted List.

In 1998, Osama Bin Laden released a fatwa directing Muslims to "kill the Americans and their allies – civilians and military".

As a result of all that, Bill Clinton ordered the assets of Osama Bin Laden frozen in August of 1998. That same month, he also attempted to kill bin Laden via cruise missile attack on an Afghan camp.

Clearly, by 98-99, Clinton had quite a good idea that Osama bin Laden was both responsible for terrorist attacks against the United States and a continuing danger to the United States.

What's more, by late 2000, we did know that Al Qaeda was behind the USS Cole attack. In fact, on page 193 of the 9/11 Commission Report, we find the following:

"the Yemenis provided strong evidence connecting the Cole attack to al Qaeda during the second half of November, identifying individual operatives whom the United States knew were part of al Qaeda. During December, the United States was able to corroborate this evidence. But the United States didn't have evidence of bin Laden's personal involvement in the attacks until Nashiri and Khallad were captured in 2002 and 2003"

So, by November we had strong evidence that it was an al Qaeda operation. By December, we had proof. The only thing we lacked was evidence that Osama bin Laden had personally authorized the attack, and we didn't get that until long after 9/11 had happened.

Of course, Osama bin Laden was the head of al Qaeda whom we'd been trying to kill off and on for a couple years, so it doesn't seem like a difficult deductive leap.

http://tinyurl.com/hsd7m

As Richard Clarke noted in his book (and as contemporary press reports indicated at the time), we knew while Clinton was in office that the USS Cole had been attacked by al-Qaeda.

This was noted by the Center for American Progress (not exactly a right-wing site), when they were reviewing the 9-11 Commission report. Evidently, the Clinton folks knew enough, according to CAP, that "Upon entering office, the Bush administration was specifically told that al Qaeda was responsible for the October 2000 bombing of the USS Cole in Yemen."

This is further confirmed by Clarke’s testimony before the Commission, where he states that, by the close of the Clinton Administration, they definitively knew that al-Qida had undertaken attacks not only on the Cole, but masterminded WTC-93 and the embassy bombings.