There are four of them:
- Counterespionage and Counterasymmetrism Directorate (“One”)
- External Security Directorate (“ExSec”, or “Two”)
- Intelligence Security Directorate (“Three”)
- Internal Security and Surveillance Directorate (“Four”)
- Fifth Directorate
(There’s also the Central Vetting Office, but it doesn’t have full Directorate status or representation on the Imperial Security Executive.)
The First Directorate started out doing simple counterespionage, disrupting and neutralizing the activities of hostile (and even friendly) intelligence services within and without the Empire. In 1513, they had counterasymmetrism added to their mandate, making operations against terrorism etal. their business too.
(So when the Grim Beeper comes to call in the 'verse, it’s probably them.)
The Second Directorate are the chief ISS offensive instrumentality. They do missions abroad in the fields of espionage, infiltration, reconnaissance, asymmetrism, preemption, assassination, and sabotage. All, of course, for the good cause of correcting problems before they occur, and in the best possible taste.
(One might compare them to the CIA, except that if they’d been running things back in the day Hitler would have mysteriously choked to death on a bratwurst back in 1925 and no-one would ever have known what might have happened. Or so they’d claim - but they are much better at this sort of thing and have never been caught at an Exploding Cigar Plot.)
The Third Directorate are responsible for intelligence security (and, as part of that, security intelligence), and are in charge of preventing penetration of the ISS and the rest of the Imperial governance by foreign intelligence. Sometimes considered the boring cousin of the directorates, they are also notorious for their leave-in-place-surround-with-3D-agents-and-feed-misinformation policy when they find a spy, about which they are quite open in order to make foreign agencies doubtful about the value of intelligence gathered from the agents they haven’t found.
(Getting a foreign agency to recall one of those unfound loyal agents and shoot them as a defector out of sheer paranoia is quite the feather in the cap for a Third agent.)
The Fourth Directorate are in charge of internal security and surveillance at a level above that which is provided for by the Watch Constabulary and Office of Investigation and Pursuit. (You might think of them as roughly analogous to the FBI, except that a large part of the FBI’s criminal mission would still be OIP business. You mostly have to be organized crime or public corruption to come to the Fourth’s attention in this respect, or otherwise exceptionally high-level; they also take the responsibility of dealing with Renegades commiting crimes abroad or crimes committed abroad against citizen-shareholders where local justice has been deemed inadequate; i.e., they run the black justice program.
They also would point out that they’re not a bunch of bunglers who charge around with tanks and machine guns; they follow the ISS unofficial mission statement of “That Snake That Bites People Who Subsequently Don’t Realize They’re Dead For Three Days? Not Subtle Enough,” and if they need to take someone in, he just goes to the bathroom and never comes back.)
And then there is the Fifth Directorate, which does not exist, but if it did, would be in charge of existential threats and everything else that falls into the category of “requiring excessionary ethics to handle”. Basically, horrors beyond mortal comprehension.