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Yes, basically a state organization that the public has no control over it and is following its own goals, often against the goals of organizations under the control of the public.

It's often taught in political classes and it isn't a conspiracy that there exists a "deep state" or "shadow goverment".

For example, the roman elite troop, the Praetorian Guards, can be classified as a "deep state", as they had their own goals and if they were not meet, then they would just kill the emperor. At the same time, the emporer and the senat had almost no control over the Praetorian Guard.