Following the Fall, she and Tomlin (the only survivor under her command) from Twilight Command make it to The Fleet. It is there that both she and Tomlin elect to desert the Colonial Military, believing that it no longer exists and that Admiral William Adama is "playing soldier" in a make believe fantasy.
Flores reforms Twilight Command as her own elite force, enlisting Spark, Devos, and Tomlin, and together they plan to escape in a Raptor from Galactica some twenty-two days prior to the discovery of New Caprica. Forewarned about this effort, Twilight Command's operation is thwarted by Kara Thrace. Following this, Adama decides to jail these conspirators, believing that they can be a useful asset in the future despite their disobedience (Battlestar Galactica: Twilight Command 2).
Twilight Command's members are released and settle New Caprica (Battlestar Galactica: Twilight Command 5), but are forced to create their own resistance force on New Caprica—separate from the resistance force under Saul Tigh—after the Cylons discover and occupy New Caprica's human population.
Operating as of the 102nd day of the Cylon occupation of New Caprica, Twilight Command kept itself outside of New Caprica City in a nearby forest and fought solely for its own survival.
At Tigh's behest, before he is taken away by the Cylons, Galen Tyrol and Samuel Anders seek out a probable location for Twilight Command and, much to their surprise, establish contact (Battlestar Galactica: Twilight Command 1).
Twilight Command is able to take out John Cavil's Centurion factory, as well as the Centurions made there, thus crippling Cavil's plans on dominating the human race. This effort gives the New Caprica denizens time to establish its own resistance and a chance for survival under the Cylon occupation (Battlestar Galactica: Twilight Command 5).