Although Sisko resented his position under the Intendant, he had no desire to become a "hero" or resist the Alliance's rule. However, when he met Kira Nerys from a mirror universe in 2370, the thought of the possibility of being free of Alliance control, combined with Kira's assertion that he was still just a slave but didn't realize it, convinced him to change his mind and reject the Intendant's authority. He helped Kira and Bashir escape from the station, and took Miles O'Brien, whom he nicknamed "Smiley," into his crew. Sisko promised to "shake things up a little" in his universe. Good to his word, he started the Terran Rebellion against the Alliance.
Sisko is stated to have died at some point between the episodes "Crossover" and "Through The Looking Glass". The precise details behind his death are unknown, but following his death, Smiley O'Brien recruited the Ben Sisko of the prime universe to complete his captain's previous mission to free Jennifer Sisko from the Alliance.