You only have part of the transcript. From the 9-11 hearing transcript from Clarke:
ROEMER: I've been very impressed with your memory, sitting through all these interviews the 9/11 commission has conducted with you. I press you, again, to try to recall how this request originated. Who might have passed this on to you at the White House situation room? Or who might have originated that request for the United States government to fly out -- how many people in this plane?
CLARKE: I don't know.
ROEMER: We don't know how many people were on a plane that flew out of this country. Who gave the final approval, then, to say yes, you're clear to go, it's all right with the United States government to go to Saudi Arabia?
CLARKE: I believe, after the FBI came back and said it was all right with them, we ran it through the decision process for all of these decisions we were making in those hours, which was the Interagency Crisis Management Group on the video conference.
I was making or coordinating a lot of decisions on 9/11 and the days immediately after. And I would love to be able to tell you who did it, who brought this proposal to me, but I don't know. Since you pressed me, the two possibilities that are most likely are either the Department of State, or the White House Chief of Staff's Office. But I don't know.
The request came from the Saudi embassy, but not directly to Clarke. It came to him through the State Department or the White House. But the decision on how to coordinate was left up to Clarke, and he put the number 2 man at the FBI in charge.
In fact he states in the portion of the transcript you posted: The request came to me and I refused to approve it.
Clarke did not receive the request from the Saudi embassy. He did not make the decision to allow the plane to fly. The request came from either the state department or the white house for them to deal with it.
Pay attention.
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