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But you are not alone in thinking Berger was at the National Archives to destroy any reference to Able Danger. The following website is great on this theory:

http://bamapachyderm.com/archives/2005/08/11/able-danger-and-911/

Here's an excerpt:
"Maybe I’m just paranoid, but I would really like to know what Berger knew about Able Danger; and if he wrote a memo, or signed off on one, that specifically related to Able Danger; and that prevented the dissemination of information that might have led to the arrest of the 9/11 hijackers before they could carry out their plans. And, could that memo–or copies–have been in the National Archives?
It is, of course, unlikely in the extreme that it still exists after his foray into the archives.

I would add this, that the documents that Berger has admitted to stealing and destroying were said by him to have been in regards to preparing remarks for the 9/11 Commission on the 1999 al Qaeda Millennium bombing attempts.
…
Would those documents directly implicate Berger as some one who had prevented Atta’s name from being passed to the FBI? Possibly. This would not mean that Berger really knew about Atta–since hundreds of memos must have crossed his desk every day–but if there was a paper trail linking Atta’s name to Berger’s office this would be embarrasing, to say the least. It would be enough to kill his reputation in a way that the actual stealing of the documents couldn’t.

But in any event, Berger’s office, at least in late 1999 and probably until he left office in early 2001, seems to be the go-between place for various agencies intent on foiling al Qaeda plots in the U.S. If we are looking for a face to put on the idiot who decided that it would be better to follow ‘policy’ rather than break it–just months after a plot to blow up LAX by al Qaeda was accidentally disrupted–I would suggest beginning an investigation there."