I have assumed that it was drafts of Clarke's after action report on Millennium security that included these criticisms of the Clinton administrations handling of security, that were purloined from the secure reading room in the Berglery.
Here's an interesting and related question: do Berger's cell phone records or the landline records of the National Archives reflect any calls he made during his visits there? If not, why did he lie about making "private" calls. If so, who did he call, and what did they talk about?