I'm actually going to take this chance to try to explain some of the mechanical aspects of the game, so they make sense when the game starts. The Agency will have access to a certain number of resources: field agents, transport vehicles, assault teams, hackers, and other, spoileriffic things. You can take pretty much any action that makes sense with the resources at your disposal: send a team to a location, attempt to trace a website to a person, start tailing a suspect, etc. Field agents can take public transportation to their objectives, but they can also use Agency transport. Agents can be assigned to direct an assault team if more finesse is required than normal. Assault teams are slightly more restricted: they don't exist, officially, and so are restricted to Agency transport if in full gear. If in disguise, they can be ferried in any available vehicle. Be aware, however, that public transport does not conform to your timetable: when the clock is ticking, a delayed flight could spell disaster. The director of the Agency has a few actions available, outside of obvious, easily-done-by-humans actions. He may attempt to gather more funds and assets for the Agency through various means. This could include official channels, bribery, and basically any other way of obtaining materiel. He can also accompany a team on a mission, or go on a mission himself. This could have benefits in terms of motivation, but be aware that getting the director killed is a Very Bad Thing, and you do not want that to happen. Ever. One of the director's real strengths comes from his ability to access the Library. The Library is, well, a library. It contains the sum of human knowledge and then some, all accessible from a computer terminal. Anything unexplained that pops up in the course of the game is probably somewhere in the Library. That's about it for now. Don't think you're restricted to the described actions. If you can't do something, I'll let you know.
tl;dr boring game mechanics stuff.