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I am not saying Atta operated independently.
I am saying that for such a complex operation
there was a general in charge
who conceived the operation
organized it,
and carried it out,
and that general was not sitting in Jalalabad
and that general was not Saddam Hussein.

Obviously Atta had outside support,
met with the Iraqis, al-Qaeda officials,
made arrangements with others
about the delivery of supplies,
sent back reports.

But he was not taking orders from superiors.

He cooked up the idea with his friends while in Germany.
Yes they all had undergone indoctrination in various places.

'Satan' thinks Al-Qaeda acts only as a recruitment agency.
I agree, though I think maybe it would be better likened
to the some kind of Masonic society.

But I do not agree that the mastermind was Saddam.

Repeat: any project of this size and magnitude
has someone in charge organizing and coordinating everything.

That person was Atta.

If you want a historical precedent,
perhaps Gavril Princip, who assassinated Archduke Ferdinand.
There were many attempts to link him with the Serbian government
but it seems likely his group acted independently
though the Serbian Secret Service probably
were informed of his intentions.

To complete the analogy.
Al Qaeda can the likened
to the pre-WWI Serbian 'Black Hand'.
A loose group of like-minded individuals
who floated about and got together
here and there
to plot against the Austrians
and others.

From all appearances, Atta was the operational commander. As such, he presumably had much latitude of action. But to call him a general is overstating things, in my view.

In your scenario, others in the Middle East were certainly aware of Atta's plans (because they were providing support). They were allowing a major attack on the U.S. to be carried out essentially in their names, therefore they would have demanded full participation in the planning and they would not have proceeded without a long-term strategy.

I don't know if the attack was directed from Iraq, or Iran, or China, or a consortium of these [or somebody else], but it must have had external direction, approval, and planning, and it must have fit well into somebody's long-term intentions.