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In 2374, Luther Sloan cast himself as the Deputy Director of Internal Affairs in a Section 31 holoprogram designed to test Julian Bashir's suitability to become a 31 member. (DS9 episode: "Inquisition")
Following the destruction of the USS Valiant, Internal Affairs launched an investigation into the actions of the Red Squad cadets. Internal Affairs criticized the decisions made by the cadets, although the public perception of them as heroes of the Dominion War made them overlook the actions of Red Squad. (DS9 short story: "Dorian's Diary")
In 2376, Starfleet Internal Affairs assigned Tiris Jast to investigate Miles O'Brien after evidence surfaced that O'Brien might have been responsible for sabotage on Deep Space 9. (DS9 - N-Vector comics: "N-Vector, Chapter 1", "N-Vector, Chapter 2")