I find it very hard to imagine that the NSA and/or CIA would have let the attacks happen, even to protect key assets and methods. Maybe they had compromised some Mossad communication channel. Or maybe they had a double agent. But what would have been worth the risk to DC and NYC?
To an extent, as with all big data systems, massive collection of data has both opportunities and risks. The risk in overcollection (e.g., the NSA type programs) is that you collect so much damn information that you are either behind in analyzing it or flat out never get there [1-2]. Combine that with (as others have noted) the lack of translators and you get what you got [3]. The old maxim* that not all data is information (DIKW) heavily applies here [4]. This whole phenomenon becomes especially problematic when you are spending all that time energy and money largely trying to predict 'black swan' events using what has happened before as what to look for in the future (e.g., the TSA as a whole or the NSA still focusing on cold war languages pre-9/11 [3]).
[1] http://www.zdnet.com/article/nsa-whistleblower-overwhelmed-w...
[2] http://apps.washingtonpost.com/g/page/world/how-the-nsa-trie...
[3] http://www.washingtontimes.com/news/2009/aug/31/lack-of-tran...
[4] https://en.wikipedia.org/wiki/DIKW_Pyramid
Edit: *fixed typo of maximum to maxim
So the NSA might have known these people were learning to fly and maybe even preparing a hijack, but until 9/11 this was not dramatic -- if and when the hijack happened, they would have been expected to fly to Cuba or something and then dealt with. Pre-9/11, airplane hijacks had become rare since their '80s and '70s heydays, maybe there was some complacency (as in "yeah these guys will never manage it, and even if they do, we'll likely get most passengers back safely anyway, let them play"). Or at least that's what a sharp Occam's razor would suggest.
The fact that the 9/11 highjackers had planned to die as part of the hijack was a game changer.
I find http://911blogger.com/news/2013-05-16/hollywood-and-911-movi... but nothing there about anything broadcast on Fox.
First episode: https://youtu.be/EjbQ-BDh4PU
Edit: the author of your link addresses the episode in the comments section, "The Lone Gunmen Pilot Episode", and says that the article you linked was only focused on things "in production" when the attack occurred.
Vince Gilligan was an Executive Producer.
The actor playing the father, George Coe, was one of the original Not Ready for Prime Time Players on SNL, then later played Ben Cheviot on "Max Headroom".
WTC was an iconic target, for sure.
And maybe the NSA and CIA weren't talking, either.
We see this all the time in large companies now, the difference is that rarely do people die as a consequence. Maybe the NASA Challenger accident is a comparable organizational breakdown.
I have always been curious about this as an organizational phenomenon. What percentage of documents are classified for actual security reasons as opposed to things like embarrassing the country or allies, covering up misconduct or outright illegal conduct, or just as the default reaction. Study would be impossible/impractical even with access, but it sure would be interesting.
> Indeed, some of the C.I.A.’s best information about Al Qaeda came from the F.B.I. In 1998, F.B.I. investigators found an essential clue—a phone number in Yemen that functioned as a virtual switchboard for the terror network. The bombers in East Africa called that number before and after the attacks; so did Osama bin Laden. The number belonged to a jihadi named Ahmed al-Hada. By combing through the records of all the calls made to and from that number, F.B.I. investigators constructed a map of Al Qaeda’s global organization. The phone line was monitored as soon as it was discovered. But the C.I.A., as the primary organization for gathering foreign intelligence, had jurisdiction over conversations on the Hada phone, and did not provide the F.B.I. with the information it was getting about Al Qaeda’s plans.
So was the NSA also monitoring the Hada phone? Or maybe providing technical support for the CIA?
The hijackers even stayed in Laurel, Maryland, from which you can literally see Alpha and Bravo.
Yet the 9/11 commission only spent three visits and a paltry amount of time up at Fort Meade and NBP, anecdotally because the commute to the Fort is too long.
Edit in reply: No, they never put the intelligence together. See here for a not-terrible summary: http://www.newyorker.com/magazine/2014/01/13/the-al-qaeda-sw...