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It has come up during the Comey hearings, bringing the term to a wide audience.
It’s a conspiracy-theory type term that started 60 years ago: It means that besides the regular U.S. government, there is a secret-ish organization of security officials across various governmental domains which work together to enforce their values and goals.
Currently, some Trump supporters are pointing to the Deep State and saying it is behind an attempt to damage the president, and the current Comey investigation is part of this attempt.