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In the year 2270, Lieutenant Commander Flynn was assigned to the USS Enterprise as chief of security. During her time aboard the Enterprise she became known to be very efficient and constantly drilled those under her command. On a personal level she also became friends with Hikaru Sulu. (TOS novel: The Entropy Effect)
By 2285, Flynn had been promoted to captain and was given command of the USS Magellanic Clouds, a long-range explorer that was given a mission to proceed towards the Andromeda Galaxy. (TOS novelizations: The Wrath of Khan, The Search for Spock)