Well, Moussaoui wasn't just some weirdo that popped up after 9/11. Keep in mind that he was already in jail on 9/11 resulting from suspicious activities at an American flight school. He'd been under surveillance by French intelligence since the mid-90s because of his radical activities. He was a previous associate of Richard Reid (the shoe bomber) and had lived in Indonesia in a house owned by a member of al Qaeda which is a home where several of the actual 9/11 hijackers had stayed for a while on their way to America.
He was wired the money from flight school from an al Qaeda financier (since captured and in U.S. custody). That same person told the Feds that he had met with Moussaoui to plan operations but ultimately it was decided not to use him for 9/11.
I don't think anybody seriously doubts the connection between Moussaoui and al Qaeda, just the connection between Moussaoui and 9/11 specifically.
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