People join these agencies because they have good hearts, and want to see the world thrive in a state of peace, equality, abundance and freedom. That being said, the "disastrous rise of misplaced power" to which President Eisenhower referred when referencing the military industrial complex, has taken a hold of these agencies, which now comprise what's known as the Deep State. The Deep State is a covert network of powerful and influential people who continue to manipulate, lie, and deceive the public for their own interests.
Oh, by the way, it's safe to assume that the Deep State also includes, as mentioned above, the agencies we don't yet know about. We know this from looking at history: The National Security Agency (NSA) was founded in 1952, its existence was hidden until the mid 1960s; Another great example is the National Reconnaissance Office, which was founded in 1960 but remained completely secret for three decades.