For security reasons the Joint Directorate would keep the military?s WMD intelligence shielded from the CIA; while it would keep the CIA?s political intelligence shielded from the Military.
This is essential to limit the espionage effort of foreign intelligence agencies by dividing the information between different agencies and keeping foreigners completely out of the staff of the Joint Directorate.
The Joint Directorate would relay the Military?s WMD information to the CIA and the CIA?s political information the military, only whenever it could fit into the big picture and help the other agency?s efforts on a strictly need to know basis.
The NSA could be employed to recruit a vast pool of Western Linguists to monitor the Islamic cadres of other agencies to make sure they aren?t working for a foreign government.
From the above it is very clear that the Joint directorate would be serving as a large research and analysis body; gathering and analyzing information from the different agencies, passing it to other agencies on a strictly need to know basis, devising a common goal for the different agencies, and then formulating a Joint plan for the achievement of that goal by dividing the effort between the different agencies.
The Different agencies would however devise their own plans regarding their own specialties such as WMD Intelligence and Political Movements etc with little or no interference from the Joint Directorate.