Aoirorentsu
Explorer
A couple of thoughts:
1) What you're describing is not really an intelligence agency per se, but a specialized law enforcement agency, somewhere in between the FBI and Interpol. It monitors supernatural activity, but that alone does not make it an intelligence agency - even your local city police office probably has crime statistics/monitoring staff. An intelligence agency, strictly speaking, is PRIMARILY concerned with gathering information. As soon as you step into enforcing the law, you are a law enforcement agency rather than an intelligence agency.
2) One thing that all intelligence agencies have to worry about is double-agents, or people who get blackmailed, bribed, or perhaps in your agency's case mind-controlled into working for the other side. To combat this, intelligence agencies compartmentalize very heavily, so no one person knows too much, and have very strong internal affairs offices (which you mention) to ferret out possible double-agents before they can do too much damage. Depending on what you want to do with your campaign and how the PCs will be interacting with the agency (particularly if the PCs work for the agency), both features could spur interesting story arcs: the Inquisitorial IA staffer can mess with PCs' attempts to be secretive, but they can also use him to take down a corrupt rival; or, the compartmentalization allows the agency to hide a larger conspiracy, and the PCs get secret info from a source within the agency who they don't even know and aren't always sure they can trust (cough X-files cough).
I will go ahead and second krupintupple's suggestion that you just focus on the parts of the organization that your PCs are likely to deal with. This will keep it mysterious and, better yet, flexible for you so you can make changes as necessary for the betterment of the campaign.
As for the multiple computers deal, I don't know
My guess is that it might be just multiple monitors, which would allow the user to look at more things at once. I haven't seen the show, though, so I'm just guessing.
Hope that helps.
1) What you're describing is not really an intelligence agency per se, but a specialized law enforcement agency, somewhere in between the FBI and Interpol. It monitors supernatural activity, but that alone does not make it an intelligence agency - even your local city police office probably has crime statistics/monitoring staff. An intelligence agency, strictly speaking, is PRIMARILY concerned with gathering information. As soon as you step into enforcing the law, you are a law enforcement agency rather than an intelligence agency.
2) One thing that all intelligence agencies have to worry about is double-agents, or people who get blackmailed, bribed, or perhaps in your agency's case mind-controlled into working for the other side. To combat this, intelligence agencies compartmentalize very heavily, so no one person knows too much, and have very strong internal affairs offices (which you mention) to ferret out possible double-agents before they can do too much damage. Depending on what you want to do with your campaign and how the PCs will be interacting with the agency (particularly if the PCs work for the agency), both features could spur interesting story arcs: the Inquisitorial IA staffer can mess with PCs' attempts to be secretive, but they can also use him to take down a corrupt rival; or, the compartmentalization allows the agency to hide a larger conspiracy, and the PCs get secret info from a source within the agency who they don't even know and aren't always sure they can trust (cough X-files cough).
I will go ahead and second krupintupple's suggestion that you just focus on the parts of the organization that your PCs are likely to deal with. This will keep it mysterious and, better yet, flexible for you so you can make changes as necessary for the betterment of the campaign.
As for the multiple computers deal, I don't know

Hope that helps.