In 2366 (around stardate 44002.3) Lieutenant Commander Benjamin Sisko is the executive officer of the USS Saratoga as it battles the Borg, led by Locutus (the former Captain Jean-Luc Picard), at Wolf 359. Its shields drained by the Borg cube, the ship sustains a direct hit, which kills most of the bridge crew save Sisko and the Bolian tactical officer, and causes the beginnings of a warp core breach: they have five minutes to evacuate the crippled vessel. Sisko orders the lieutenant to help the surviving civilians to the escape pods and goes in search of his own family.
In his quarters, Sisko finds his young son Jake, and his wife Jennifer, buried under a pile of rubble. Although he is able to rescue Jake, Jennifer remains trapped. As Sisko digs through the rubble, the Bolian lieutenant scans Jennifer with a tricorder and finds she is already dead. Sisko ignores the lieutenant’s desperate pleas to escape and continues trying to rescue his wife; he is ultimately dragged away screaming to an escape pod. Together with Jake and the other survivors, he watches from the escape pod as the Saratoga is destroyed.
Stardate 46379.1: Three Years Later
Commander Benjamin Sisko approaches Jake, now a teenager, who is fishing from a lake in an Earth-like setting. Jake seems dismayed they will soon be living on a space station rather than Bajor, the planet the station orbits. Sisko assures Jake that he will have fun and meet lots of new friends, but they are interrupted by a voice from the bridge, informing Sisko that they are approaching Deep Space 9 and will be docking in seven minutes. Sisko ends the program and they leave the holodeck. Walking past a window, Sisko and Jake get their first look at Deep Space 9, the former Cardassian mining station which will now be their new home.
Sisko and Jake arrive at Deep Space 9 and are dismayed to find the station in a state of disarray, ransacked by the Cardassians following the Occupation of Bajor; the planet itself is apparently in a similar state. Neither Benjamin nor his son find the place, or their quarters, accommodating, but they decide to “rough it” for the time being. Chief O’Brien reports that most systems are offline and a lot of vital equipment is missing or severely damaged. O’Brien also notes that Captain Picard wishes to meet with Sisko, a prospect the commander does not seem to relish.
Ascending to Ops, Sisko enters the prefect’s office and finds his Bajoran liaison officer, Major Kira Nerys, in heated argument with one of the Provisional Government’s ministers, whom she hangs up on. Kira, a former member of the Bajoran Resistance, is openly hostile to the idea of another foreign power occupying Bajor. When Sisko says the Federation is only there to assist the Bajorans, she retorts that the Cardassians said the same thing when they arrived sixty years earlier.
Their conversation is interrupted by an alarm from the Promenade, where Kira and Sisko capture a Markalian looter and his accomplice, a young Ferengi named Nog. Here, Sisko also meets a shapeshifter named Odo, the station’s security chief, who aids in the apprehension of the two criminals. Quark, Nog’s uncle and the proprietor of the local bar, urges Sisko to release Nog into his custody so the Ferengi may evacuate, but Sisko refuses, appearing to have something else in mind. Before he can elaborate to Kira, he is reminded that Captain Picard is waiting to meet with him. As he cannot put it off any longer, he heads for the Enterprise. Sisko assures Kira that the meeting will not take long.
When Sisko meets with Picard in the observation lounge, it is now Sisko’s turn to be brusque and distrusting. He begins by “re-introducing” himself, mentioning that he has already “met” Picard at the Battle of Wolf 359. Picard is obviously troubled by his memories of the event, so he begins discussing the havoc wreaked upon Bajor by the Cardassians. Bajor has applied for Federation membership, however their entrance will not be simple; with the Cardassians gone, several factions are now fighting for control of the planet. He tells Sisko that his mission aboard the station is to do everything short of violating the Prime Directive to secure Bajor’s entrance into the Federation. Picard then notes that Sisko had objections to taking the assignment, and Sisko replies with barely-restrained anger that he’s raising his son alone and that a damaged space station is not the ideal environment. Sisko also says that he is thinking of resigning his Starfleet commission to return to Earth for civilian service, but until he makes the decision he will do his job to the best of his ability. The conversation is dominated by thinly-veiled hostility on Sisko’s part, as he faces the man he holds responsible for the death of his wife. Picard dismisses Sisko.
Later, in Odo’s security office, Sisko and Odo interview Quark, encouraging him to stay on the station and reopen his establishment. The Promenade is the vital heart of life on the station, and someone has to step forward and lead the other vendors in rebuilding. As Quark is less than eager to stay – citing that “when governments fall, people like me are lined up and shot” – Sisko uses the incarcerated Nog as a bargaining chip, offering to free Nog if Quark agrees to his terms. Odo starts to warm up to the new Starfleet commander.
In a corridor, Kira is doing her part to clean the mess left behind by the Cardassians. She tells Sisko that in the refugee camps, everyone was used to do what was needed, regardless of who they were, and wonders if starfleet officiers do get their hands dirty sometimes. Sisko, without a word, picks up a piece of debris and puts it in the bin, showing his hands to Kira to proove that indeed, he can get them dirty.
Kira tells Sisko that she believes the provisional government will be gone in a week, and so will the Federation, and that the planet will be left to civil war. She expresses her belief that Kai Opaka, the spiritual leader of Bajor, is their only hope to unite the people and keep the Provisional Government intact.
When Sisko meets the kai on Bajor, she urges him to explore his pagh, or life-force, and declares Sisko to be the Emissary of the Prophets, though she doesn’t tell him everything at first. She leads him to the Orb of Prophecy and Change, which grants him his first orb experience: he is mentally transported to Gilgo Beach, years earlier (circa 2354), at the time and place he met Jennifer, his wife. He re-lives the moment of their first encounter in vivid detail, promising to prepare his father‘s famous Aubergine stew for dinner, and is distraught when the vision ends.
As Kai Opaka shuts away the Orb safely in its container, she explains that this Orb is one of nine known Orbs that have appeared in the skies over Bajor in the last ten thousand years; the Cardassians took the other eight. She also informs Sisko that his destiny, whether he believes it or not, consists entirely of finding the Celestial Temple of the Prophets, from where the orbs originated. To help him in his task, she gives him the Orb for further study.
Back on DS9, Sisko finds his son sleeping on the floor, still thinking of the image of his wife. Kira soon calls him to the Promenade, where he finds Quark has indeed unpacked and is entertaining the very diverse array of people on the station. He gets a drink and Quark implies he agrees to Sisko’s terms.
Sisko then greets his new chief medical officer, Doctor Julian Bashir, who is obviously smitten with Jadzia Dax, the station’s new chief science officer. Sisko’s meeting with Dax is really a reunion ; Dax is a Trill symbiont whom Sisko knew as Curzon Dax years earlier. Bashir offends Kira by referring to his new assignment as “frontier medicine”; to Kira, Bajor is home, not some frontier in the wilderness. Sisko quickly puts his old friend Dax to use, asking her to conduct research on the Orb and leaving her alone in the science lab. When she touches the Orb, it grows extremely bright and gives her a vision of her own.
From high above, she sees herself (as the un-joined Jadzia) lying on an operating table, receiving the Dax symbiont from a dying Curzon, realizing the first moment of her new self-awareness. The vision has a noticeably powerful effect on her emotionally, as strong as Sisko’s vision of Jennifer.
On the Enterprise, Miles O’Brien stands outside the captain’s ready room on the bridge, deciding whether to go inside or not. He decides not to, and after a final look at the bridge heads to transporter room 3. Upon entering, he asks Ensign Maggie Hubbell to beam him to the transporter pad in Ops. Just before he transports to the station, Captain Picard walks in, and dismisses the ensign. Picard notes that transporter room 3 is the chief’s favorite one to use, and says that life on the Enterprise won’t be the same without him. O’Brien smiles, and requests permission to disembark. Picard operates the transporter console and beams O’Brien to the station. For a moment, Picard quietly laments the loss of his long time transporter chief and leaves the room. The Enterprise then sets off for the Lapolis system.
Barely has the Enterprise left orbit than a Cardassian warship enters the system, transmitting fulsome good wishes from its commander, Gul Dukat – the former Cardassian Prefect of Bajor. Sisko hosts Dukat in his office (which used to be Dukat’s office just two weeks prior, when the station was still under Cardassian control). With great diplomacy, Dukat “welcomes” the Federation to the region and pledges his “support” to their efforts to rehabilitate Bajor (especially in light of the fact that the Enterprise has departed the region). In his unctuous manner, Dukat fishes for information about the Orb Sisko brought to the station, as he had believed that the eight “acquired” by the Cardassians were the only ones in existence. He offers to share what the Cardassians have learned from those eight, but Sisko coolly says he knows nothing about any Orb. Smiling politely, Dukat says his ship will remain in system for a few days, in case Sisko changes his mind, and asks Sisko’s permission for his men to enjoy the services on the Promenade.
In her lab, Dax has plotted a central location common to the pathways of all the known Orbs, the Denorios belt, a charged plasma field. Sisko is intrigued and wants to take a closer look, but is wary of being followed by the Cardassians. So he concocts a ruse…
In Quark’s, the Cardassians are winning heavily at the dabo tables, when Kira strides in and announces the bar is being closed until further notice. Quark assures his customers that it is only temporary, and one of his waiters hands them a tote bag to carry their winnings back to their ship. The “bag” is actually Odo; once aboard the ship, he sabotages their computers, disabling their sensors and engines, allowing Sisko and Dax to depart in the runabout USS Rio Grande. Kira tells O’Brien to beam Odo back to the station, but O’Brien is having trouble operating the Cardassian transporter. When the machine refuses to respond to his commands, he kicks it in frustration – which works, energizing Odo back.