The government in my world covers the entire Earth, but is run by 3 separate, cooperating continental governments (Europe, North and Central Africa, and Australasia). The rest of the world is a nuclear wasteland. There is a highly feared Inquisition, famous for highly effective interrogations, frequent executions and terrible tortures.

They control a commando force called the Interrogen to 'combat, capture and control.' The heads of the Inquisition in their respective continents are considered to be nearly as powerful as the President of the Continent. There is no military per se, but a force called the 'Civil Defense Force' which is controlled by the President and counters terrorism, provides security and acts as a regular police in normal situations. It is also not nearly as powerful as a modern military, but still outnumbers the Interrogen by a 1:50 ratio. Due to a fuel crisis in the future, vehicles are pretty rare. Basically, all the investigation and counter terrorism/counter rebellion, along with fighting major organisational crime, is done by the Interrogen. In cases of emergency, high-ranked Inquisitors can control a portion of the CDF.

My question is, this Inquisition being a highly powerful secret police, how would it go about tackling major threats to the government, especially in a discreet manner and with enough power to be able to have a lot of free will(acting autonomously without being controlled by the government)?

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    $\begingroup$ Welcome to Worldbuilding.SE! We're glad you could join us! When you have a moment, please click here to learn more about our culture and take our tour. You're asking what we call a high concept question, which isn't a good fit for our site. Stack Exchange's model is one-specific-question/one-best-answer and the question is expected to be narrowly scoped to be reasonably answered in a page or two of text. As written, this is much too broad. Can you narrow the question? $\endgroup$ – JBH Feb 23 '19 at 19:58
  • $\begingroup$ Secret police by most names are usually political organs, not military. The functions that your secret police (and normal police, and other government entities) carry out will be defined, coordinated, and synchronized by the political leadership. You (not us) must answer the question "what do the political leaders of my world want?" For example, if they want rule of law, then secret police will be rare and won't do much at all. If they want to maintain their position, power, and corrupt perks, then the secret police will be very, very busy and have a wide range of oppressive activities. $\endgroup$ – user535733 Feb 23 '19 at 21:12
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    $\begingroup$ "There is a highly respected and feared Inquisition, famous for highly effective interrogations, frequent executions and terrible tortures." You seem to assume that we have some sort of intuitive understanding of what you mean by "an Inquisition". We don't. Additionally, "respected and feared" is a most unusual combination; "hated and feared", maybe. (And a "commando force" is most definitely not some sort of secret police, or maybe I should say that any kind of functional secret police does not look, behave or operate like a commando force.) $\endgroup$ – AlexP Feb 23 '19 at 21:42
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    $\begingroup$ Can you give us some idea of the overall population numbers, and the technology level? Very often, those who control the means of production are usually the power brokers, and usually there is a security force that provides protection for the means of production. $\endgroup$ – Justin Thyme the Second Feb 24 '19 at 1:22
  • $\begingroup$ Despite the post-apocalyptic setting, your Inquisition, the Interrogen, will operate like any secret police combined with security services for counter-terrorism work. History is your guide. Organisations using torture & execution as their working methods are depressing the same. Sounds more like an international version of the Nazi SS. $\endgroup$ – a4android Feb 24 '19 at 3:14