The Emissary of the Prophets is Benjamin Sisko's identity to millions of Bajorans. It was his destiny from birth, as he was part Prophet as his mother Sarah Sisko was inhabited by a Prophet to make sure she conceived and gave birth to him. (DS9 episodes: "Image in the Sand", "Shadows and Symbols")
The arrival of the Emissary was predicted by several Bajoran writers, who wrote what they saw in several Prophecies. Sisko was revealed to be the Emissary when he met with Kai Opaka Sulan shortly after taking command of Deep Space 9 in 2369. Sisko later found the Bajoran wormhole/Celestial Temple, something that only the Emissary could do. (DS9 episode: "Emissary")
In 2372, Akorem Laan was sent forward in time from the 22nd century after entering the wormhole. As Akorem was the first to enter the Celestial Temple and was a Bajoran, Sisko was more than happy to stand aside. However, Akorem and the Bajorans began introducing types of culture from Akorem's time that had disappeared from use, including the d'jarra. This was prohibited under the Articles of the Federation and Bajor's entry into the United Federation of Planets looked to be on the verge of failing. Sisko took Akorem into the wormhole, where the Prophets confirmed Sisko as their Emissary. (DS9 episode: "Accession")
In late 2375, the Prophets began preparing Sisko for his greatest trial which he would soon face. Sarah warned him that marrying Kasidy Yates would bring nothing but sorrow. (DS9 episodes: "Penumbra", "'Til Death Do Us Part")
Sisko later discovered that the "Trial" was stopping Skrain Dukat and Winn Adami from releasing the Pah-wraith from the Fire Caves and bringing about the Restoration. Winn had poisoned Dukat as a sacrfice to the Pah-wraith, although they resurrected him and gave him supernatural powers. Sisko was no match for Dukat in this way, although he used his nemesis' brief moment of distraction while killing Winn to throw himself and his enemy into the fires. Dukat and the Pah-wraith were sealed away and Sisko was brought to the Celestial Temple, where his mother welcomed him home. Sisko planned to stay there and learn from the Prophets, but promised Kasidy he would return. (DS9 episode: "What You Leave Behind")
In 2377, Sisko encountered the Orb of Souls, which led him to meet with seven other individuals named Benjamin Sisko, each from an alternate reality. He learned here that Benjamin Sisko is meant to become the Emissary in every reality, not just his own, and that Benjamin Sisko is always born by the Prophets' design specifically to fill this role. (DS9 novel: Fearful Symmetry)
In the mirror universe, Benjamin Sisko died in 2371 without becoming Emissary. However, Iliana Ghemor became the Emissary in January 2377. (DS9 novel: The Soul Key, ST - Mirror Universe novel: Rise Like Lions)
In January 2377, the Sisko of the primary universe had an orb experience using the Orb of Souls. There, he communed with seven other Benjamin Siskos from different parallel universes, who like himself, had been drawn to Bajor at some point during their lives and become the Emissary of the Prophets. The eight Emissaries had been drawn together to chastise Sisko for not having played his role in helping his mirror universe counterpart become the Emissary in that universe. The alternate Siskos at this meeting were:
- Ambassador Benjamin Sisko, a diplomat in the Federation Diplomatic Corps, who has lost his wife Jennifer Sisko in a Kohn-Ma attack on Cardassia Prime while he was negotiating a Cardassian withdrawal from Bajor. Unlike his primary universe counterpart, he was clean shaven in 2377.
- Fleet Captain Benjamin Sisko, a man distinguished by a scar across his sightless right eye, given to him by a father who had betrayed him. This Sisko served as the military governor of Bajor in a version of the mirror universe in which the Terran Empire never fell. He wore a dagger which was sheathed in the sashlike belt of his gaudy metallic uniform.
- Doctor Benjamin Sisko, a member of the Daystrom Institute who discovered the Bajoran wormhole after an accident which took his sister Judith Sisko's life. In his reality, the discovery of the wormhole led to a social revolution which had begun the dissolution of galactic nation-states in favor of a loose but stable interstellar sprawl where information was freely exchanged. Unlike his primary universe counterpart, he wore a full beard.
- Colonel Benjamin Sisko, an officer in the Celestial Union, a planetary alliance with Bajor at its centre and whose numerous members included Earth and Cardassia Prime. He lost his parents and discovered the wormhole during a savage war with the Tholians.
- Admiral Benjamin Sisko, a member of Starfleet in a Federation that had absorbed many of its former enemies including the Klingons, the Romulans, the Cardassians, the Tzenkethi and the Breen. He was a widower and the hero of the Battle of Wolf 359.
- Sisko of Borg, a Borg drone from a reality where the Federation had fallen to the Borg. Despite his assimilation, he still found his way to Bajor and discovered the Bajoran wormhole.
- Benjamin Sisko, a member of Starfleet who lost his only son Jake Sisko aboard the USS Saratoga during the Battle of Wolf 359, an event which destroyed his marriage, career and almost his will to live. (DS9 novel: Fearful Symmetry)