In the mirror universe, Benjamin Sisko (played by Avery Brooks) was a Terran privateer who worked his way out of the Klingon-Cardassian Alliance's slave mines and earned himself a position serving the Intendant of Bajor, Kira Nerys. Sisko was Kira's lover, and commanded a small raiding ship crewed by other Terrans, and charged with collecting "duties" from passing ships. (In other words, Sisko was a real-life pirate.)

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 "our" 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. (DS9: "Crossover") Sisko was good to his word; he started the Terran Rebellion against the Alliance.

Although Sisko was a great tactician, he was a stubborn, abrasive man that didn't get along with anyone very well. He was married to Jennifer Sisko, a privileged Human scientist, but he hardly got along with her at all, and as of 2371 hadn't seen her in over five years. According to Smiley, they never should have been married in the first place. Sisko was the lover of Jadzia Dax, whom he recruited to join the rebellion.

In early 2371, Sisko was killed during a mission to convince his wife to leave Terok Nor and work for the rebellion. Desperate to complete Sisko's mission, Smiley recruited the Benjamin Sisko from "our" universe to finish his task. Sisko assumed the guise of his deceased counterpart, successfully fooling everyone from Julian Bashir to Elim Garak to the Intendant herself. (DS9: "Through the Looking Glass")

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