Image In the Sand
It's been three months since Sisko left and Kira struggles to keep control of the station while the spiritual Bajorans try to deal with the apparent demise of their gods. Back on earth, Benjamin and Jake are still working at their father/grand-father's restaurant in New Orleans while Benjamin continues to search for answers about the disappearance of the prophets, until one night while playing the piano, his baseball falls to the floor and he sees a vision of a woman's face in the sand. After using a photo-fit kit to make a drawing, Jake recognizes it as a picture of a woman he's recently found a photo of while clearing out. Both are amazed at the reaction of Benjamin's father, who refuses to discuss who the woman is. Eventually Benjamin persuades him too, and he discovers that the woman he always thought was his mother wasn't, and that this woman, Sarah is actually his true mother.
Shadows and Symbols
As Sisko searches for the Orb of the Emissary, Kira prepares a blockade preventing the Romulans near the Bajoran moon Durna. Meanwhile, Worf and Martok lead a suicide mission in Jadzia's name.
The presence of Ezri Dax on DS9 causes problems for Worf. Meanwhile, Garak suffers an incapacitating breakdown.
Take Me Out To the Holo-Suite
A Vulcan Starfleet officer insists his race is superior, and to prove it, he challenges Sisko to a game of baseball in the holosuite.
A genetically enhanced woman who has fallen into a catatonic state is treated by Dr. Bashir, who falls in love with her.
Treachery, Faith, and the Great River
A clone of Weyoun seeking asylum submits himself to Odo as a prisoner, offering invaluable information about the Dominion.
Once More Unto the Breach
With nowhere to turn and old age having made him obsolete, Klingon legend Kor asks Worf to help him find one last glorious battle.
The Siege of AR-558
Sisko's crew is diverted to the front lines, where, alongside war-torn Starfleet officers, they must make a stand against a Jem'Hadar assault.
Kira is kidnapped by a Bajoran pah-wraith cult led by Dukat.
It's Only a Paper Moon
Mentally and emotionally scarred by his combat injuries, Nog seeks comfort in the holographic fantasy world of Vic Fontaine.
A search for O'Brien, who has gone missing somewhere near Ezri's home world, reunites Ezri with her family and their troubles.
The Emperorís New Cloak
Grand Nagus 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 that 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.
Field of Fire
Ezri summons a homicidal Joran Dax to understand the mind of a killer.
A changeling asked Odo to leave the station and join his search for other space-shifters.
The crew attempts a daring heist of a mob-run holosuite casino.
Inter Arma Enim Silent Leges
On the eve of Dr. Bashir's departure for a conference on the Romulan homeworld, he's visited by Sloan, the director of Section 21, 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 31, 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.
Till Death Do Us Part
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 will 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 Changing Face of Evil
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.
When it Rains...
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.
Tracking Into the Wind
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. Extreme Measures
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 31 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.
The Dogs of War
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 message 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 31--an unsanctioned extremist organization within the Federation--but promises Sisko he won't take matters into his own hands.
What You Leave Behind, Part 1 and 2
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.