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Three months after a possessed Gul Dukat killed Jadzia Dax and sealed the wormhole, life on Deep Space Nine has changed. Kira, the acting commander, is upset when Admiral Ross informs her that the Romulans will set up a station office, while Sisko has retreated to Earth to contemplate a way of contacting the Bajoran Prophets - the aliens who reside within the wormhole. When the vision of a woman's face, buried in the sand, appears to Sisko, he sketches her, and Jake recognizes her from one of his grandfather's photos.
Sisko meets Ezri, the new host of the Dax symbiont, before departing Earth for the planet Tyree with his father, Joseph, and son Jake. Ezri wished to accompany them on their search for Bajor's mythical Orb of the Emissary, which Sisko has been led to believe exists. Back at the station, Kira prepares a blockade to stop the Romulans, who have placed weapons on a Bajoran moon. On a Klingon ship, Worf, O'Brien, Bashir, and Quark embark on a mission of their own: to destroy a Dominion shipyard, thus securing a place for the spirit of Worf's dead wife Jadzia in the sacred Klingon afterlife of Sto-vo-kor.
In addition to coping with the memories of her ``past lives'', Ezri Dax must deal with the range of rections fer presence generates. Kira awkwardly tries to make conversation; Sisko is happy to have his old friend back; Quark flirts with her; and Worf, pained by the memory of his dead wife Jadzia, which Ezri's presence provokes, makes it clear he wants nothing to do with her. Elsewhere, Garak inexplicably collapses and is rushed to Bashir's care.
Vulcan Captain Solok brings his starship to Deep Space Nine for repairs made necessary from combat skirmishes. Convinced his all-Vulcan crew is the finest in the fleet, he challenges former classmate and longtime rival Sisko to a baseball game on the Holosuite. With only two weeks to whip his team into shape, Sisko vows he's going to beat Solok - even though Jake is the only other person residing on the station who has ever played baseball.
A group of genetically enhanced humans, once under Bashir's care, escape from their medical facility home in the hopes that the doctor - who himself was genetically engineered as a child - can cure their friend Sarina. Her enhancements left her in a catatonic state, and Bashir attempts an untried procedure on her brain that initially appears to have no effect. However, a few days later, Sarina speaks for the first time.
Odo is lured to a secret meeting site, where he finds himself face to face with Weyoun, the Vorta leader of the enemy Dominion. Weyoun announces that he's decided to defect and, in exchange for asylum, he promises to provide valuable information that could help the Federation win the war. After the two board Odo's Runabout, the ship is hailed by the Cardassians. Odo is shocked when the monitor displays Weyoun standing beside Damar.
To Worf's surprise, he is paid a visit by Kor, an aging Klingon war hero. Kor admits that his ambition has earned him countless enemies, and that consequently he has been unable to secure the command of a ship. Worf promises to find him a miltary command, and approaches General Martok with the request - which is angrily refused. Martok explains that years earlier Kor had denied Martok officer status because he was descended from a common house. Undaunted, Worf appoints Kor as a third officer on the Ch'Tang, Martok's flagship, where he is treated with awe by the crew - much to Martok's chagrin.
While making a supply run to the front lines, on the barren planet AR-558, Sisko encounters Starfleet troops that have been decimated during their five-month occupation of the largest Dominion communications array in the sector. If they can figure out how it works, Starfleet will be able to tap into Dominion transmissions. In addition to daily skirmishes with the enemy, the shell-shcoked forces are constantly threatened by "Houdinis" - anti-personnel mines that "hide" in subspace, then explode without warning. Determined to help commanding officer Nadia Larkin and her troops, Sisko stuns his crew by announcing that they're staying at the site indefinitely.
Vedek Fala, a Bajoran monk and Kira's former teacher, pays her an unexpected visit. He gives Kira a crystal which transports her to Empok Nor, where, to her horror, she is met by her old enemy Dukat - a Cardassian who oversaw the occupation of Bajor. He is now the leader of a Bajoran religious faction which worships the Pah-wraiths - the corporeal enemies of Bajor's prophets. Dukat want Kira to join his followers on the abandoned Cardassian space station.
After losing his leg in battle, a somber Nog returns to the space station to recuperate. The crew try their best to cheer him up, but the young ensign is struggling, both emotionally and physically, to cope with his disability, even though his new biosynthetic leg works perfectly. After pushing away those who try the most diligently to help, Nog decides to take his medical leave in the Holosuite world of 1962 Las Vegas lounge singer Vic Fontaine.
Sisko is furious when he learns O'Brien has vanished while on a secret trip to New Sydney, where he was searching for the widow of a criminal named Bilby, whom he befriended while undercover. Because Ezri's family owns a mining operation in the system, Sisko asks her to help find O'Brien. Ezri returns home, where she's reunited with her domineering mother, Yanas Tigan - a shrewd business woman - and her brothers Norvo and Janel, who work for the business.
Grand Negus Zek, the ruler of the Ferengi empire and paramour to Quark and Rom's mother, disappears while on a business trip to the Alternate Universe. Ezri's counterpart from the universe delivers word that Zek is a prisoner of the evil Alliance and will be killed unless Quark can secure a cloaking device, which renders a ship invisible. Quark and Rom steal one from a Klingon vessel, then accompany Ezri back to the Alternate Universe to retrieve Zek.
A young lieutenant named Ilario is found dead in his quarters. An investigation reveals he was shot by a TR-116 rifle, a weapon developed but never mass-produced by Starfleet. Meanwhile, Ezri confronts one of Dax's previous incarnations in a dream: Joran, a self-professed murderer, urges Ezri to channel his disturbing memories and enable him to assist her in apprehending Ilario's killer. When Ezri awakens, she learns that a second murder has occurred.
Odo returns from a conference with an unexpected guest: a Changeling who tracked and boarded his Runabout. Odo recognizes him as one of ``the hundred'' shapeshifters who were, like himself, sent out as infants into the galaxy to learn about other species. Back at the station, Sisko warily releases the visitor to Odo's custody. The Changeling, known as Laas, queries Odo about their unique species - with which Laas has made no contact since his infancy - and ``the Link'', a Changeling ritual that allows shapeshifters to meld with one another and thereby form a single, sentient collective entity.
While relaxing in Vic Fontaine's Las Vegas holosuite lounge, O'Brien and Bashir are surprised by the arrival of mobster Frankie Eyes, who announces that he has bought Vic's hotel. After he fires Vic, the crew learns that Frankie was created by Vic's designer. Upset by Frankie's behaviour, and by the knowledge that the lounge's atmosphere will now change, the crew desides it must rid him from the program. But he must be eliminated in a way what is period-specific to Fontaine's era: 1962. The task takes on greater urgency when Vic is beaten up.
On the eve of Dr. Bashir's departure for a conference on the Romulan homeworld, he's visited by Sloan, the director of Section Thirty-one, a secret and unsanctioned extremist entity within Starfleet Intelligence. Sloan asks a reluctant Bashir to gather information on the Romulan leadership. Bashir reports the request to Sisko, who worries that although Starfleet Command has officially condemned Section Thirty-one, someone in its membership may actually be protecting the group. After consulting with Admiral Ross, Sisko advises Bashir to play along with Sloan in order to determine Sloan's motivations.
As Sisko revels in the purchase of Bajoran land, where he hopes to finally build his dream house, word reaches the station that worf is missing in action after a fierce battle with the Dominion. Due to strategic concerns, Sisko calls off the search party before Worf can be found. Overcome by memories of Jadzia's life with Worf, Ezri steals a runabout and goes in search of Worf herself.
Kai Winn arrives at the station to ``assist'' Sisko with his wedding, and he admits the Prophets warned he would face a great trial in his future. Later, Winn has a long-awaited vision from the Prophets, who reveal that a ``Guide'' will soon visit her; the Prophets hope that, together, the two wil lead Bajor's Restoration. Shortly before Sisko tells Kasidy that they must call off their wedding, Dukat, surgically altered to look like a Bajoran, appears of the Promenade.
Worf and Ezri are beamed aboard a Jem'Hadar ship, where the Female Shapeshifter and Thot Gor, the respective leaders of the new Dominion-Breen alliance, prepare to sign a treaty designed to destroy the Federation and end the war. However, Damar objects to signing it because of concessions, made to Thot Gor, which could harm Cardassia. Meanwhile, Kai Winn and Dukat seal their bond by pledging to restore Bajor - even if the Emissary stands in their way.
The crew's relief at Worf and Ezri's safe return is tempered by reports that the Breen have attacked Starfleet Headquarters on Earth. While Dominion and Breen commanders exult in their sneak attack, their supposed ally - Cardassian leader Damar - secretly plots to free his homeland from Dominion occupation. Meanwhile, on Bajor, Dukat tells Kai Winn she must release the Pah-wraiths - the corporeal enemies of her people's gods - from the planet's fire caves by reading the ancient forbidden text of the Kosst Amojan.
Eager to aid Damar's rebel movement on his homeworld against the Dominion, Sisko orders Kira to put her antipathy for the Cardassian aside and train his staff in resistance tactics. Bashir asks Odo to assist in his medical project by donating the Changeling-equivalent of a skin sample. On Bajor, Kai Winn studies the forbidden text of the Kosst Amojan to learn how to release the evil Pah-wraiths. Hoping to ease Cardassian sentiment against the Bajoran Kira, Sisko givers her a Starfleet commission and uniform.
While Kira reviews tactical plans with the Cardassian Resistance leaders, Odo returns from a mission, weakened by the disease that's ravaging his race. At the station, Bashir works through the night, trying to find a cure for Odo, while Sisko reproves Chancellor Gowron for reckless attacks which left General Martok injured. Back at the rebel headquarters, Kira, eager to discover why the Federation's Klingon ships aren't damaged by Breen-Dominion technology, proposes stealing the enemy's weaponry so that the Federation can engineer a countermeasure.
When Kira brings a terminally ill Odo back to the station for medical treatment, he orders her to leave him and return to help the Cardassian Resistance. Later, O'Brien and Bashir inform Sisko of their plan to lure a Section Thirty-one operative, who may hold the cure to Odo's disease, to the station. The scheme works when Sloan, the director of the unsanctioned Starfleet extremist organization that infected Odo - as part of a genocidal plot against his people - arrives. But when Bashir places a Romulan mind probe on the agent, who refuses to give information regarding a cure, Sloan attempts suicide in the science lab by activating a neuro-depolarizing device in his brain.
While Sisko takes command of a new ship named in honor of the Defiant, Kira, Garak and Damar barely escape a Dominion ambush on Cardassia and are forced into hiding. Quark receives a static-filled messade from Grand Nagus Zek, the Ferengi leader, that he's been named Zek's successor. Now cured of the deadly Changeling virus, Odo is outraged to learn that he was infected by Section Thirty-one - an unsanctioned extremist organization within the Federation - but promises Sisko he won't take matters into his own hands.
On the eve of battle, Bashir and Ezri spend the night together. Later, with Sisko in command, the Defiant joins the Federation-Klingon-Romulan fleet as the invasion of Cardassia is launched. On Cardassia Prime, Kira, Damar and Garak discuss Resistance plans to sabotage the Dominion's power and communication centers. On Bajor, Kai Winn asks Dukat to join her when she releases the Pah-wraiths from the Fire Caves, and Dukat vows to destroy Sisko.
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