Berger was acting on the orders of Bill Clinton, and for one of two reasons (maybe both). Either Clinton didn't want the world to know that he was asleep at the wheel in the fight against terrorism (theft and destruction of certain documents), or he wanted to find out what documents the commission possessed so Berger would be able to give a heads-up to all the members of his administration who were to testify before the commission, i.e. how to spin their answers.
The Clintonistas were able to put the 9/11 Commission to sleep. The Bush Administration could have saved itself some grief if it had announced the Berger investigation when it first began. It would have also spared us the Richard Clarke tap-dance on the witness table.
Clinton Testifies Before 9/11 Panel
excerpt:
A person familiar with the session said Clinton told the commission he did not order retaliatory military strikes after the bombing of the USS Cole (search) in October 2000 because he could not get "a clear, firm judgment of responsibility" from U.S. intelligence before he left office the following January.
~snip~
I hope there isn't any missing document that would disprove this assertion...
Remember the Rats wanted to politicize the intell to take down Bush. Many classified pieces of info were leaking to the public. I theorize that Berger was told to get in there to remove anything that could ultimately come back to bite Bubba in that scenario. Then, the 9/11 Commission was seated and more speicific *notes* and docs had to be removed to cover a whole bunch of booty.