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The Expeditionary Fleet (or Ex-Fleet) is, according to Julian DiMarco, a cover for the Colonial Fleet to conduct black operations (Battlestar Galactica: Season Zero 1).
Neither DiMarco nor his crew knew of this before embarking on a survey of a planet in Neutral Space. A majority of Ex-Fleet ship personnel are civilians, with the ships provisioned for deep space exploration, in addition to bombs for fault-line exploitation and land clearing (Battlestar Galactica: Season Zero 2).
Ships of the Ex-Fleet are answerable to a Colonial Fleet liaison (Battlestar Galactica: Season Zero 2).