"Sacrifice of Angels" is the final episode of the six-part story that begins the show's sixth season. At the end of season five, Dominion forces led by Gul Dukat and Weyoun invaded Bajoran space, forcing the Starfleet crew manning Deep Space Nine to abandon the station.
Captain Sisko, aboard the starship Defiant, commands a fleet ordered to retake Deep Space Nine before the Dominion destroys a minefield blocking the Bajoran wormhole, which links the Alpha Quadrant to Dominion territory in the Gamma Quadrant.
Sisko orders Federation fighters to attack the Cardassian warships making up a portion of the Dominion fleet, hoping the more emotional Cardassians will pursue the ships, creating a hole in the Dominion lines.
Aboard Deep Space Nine, Gul Dukat is aware of Sisko's ruse. He informs the other Dominion leaders, saying that he will allow the bulk of the Federation fleet to penetrate behind Dominion lines, then use superior numbers to surround the enemy. The female changeling notes that Dukat's boasting has not led to the destruction of the Federation minefield, which is several weeks behind schedule.
Once the Dominion leaders leave, Damar asks Dukat's permission to detain Major Kira, Jake Sisko and Leeta. Damar believes they are behind a sabotage attempt by Rom, a Ferengi technician. Dukat grants Damar's request. Damar also advises Dukat keep his daughter, Tora Ziyal, confined to quarters "for her own safety." Damar does not trust Ziyal because she is a close friend of Major Kira. Dukat refuses to listen to Damar's advice.
Sisko sends additional fighters against the Cardassian cruisers. Dukat allows some of his ships to go after them, opening a hole in the Cardassian lines. Knowing Dukat is setting a trap, Sisko nonetheless orders his ships forward, desperate to reach Deep Space Nine. As Sisko's efforts devolve into chaos, Odo is confronted by the female shapeshifter, who informs him that Kira has been arrested and will be executed.
As Jem'Hadar warships surround the Defiant, disruptor fire destroys them. A Klingon fleet, led by Worf and Martok, has arrived. They clear a path for the Defiant, though the rest of the allies are unable to follow.
Quark corners Ziyal, asking her to help him free Jake, Kira, Rom and Leeta. The two free the group. Kira organizes the sabotage of the station's weapons, and she and Rom set off for the station's core, pursued by Jem'Hadar forces. They are cornered in a cargo bay, but are rescued by Odo and Bajoran security. Odo's men cover them as they enter a maintenance shaft to sabotage the weapons.
Rom sabotages the weapons, but too late. Dukat orders the minefield destroyed, which is witnessed by Sisko aboard the just-arrived Defiant. Sisko orders the Defiant into the wormhole, where the crew encounters a massive Dominion fleet. As Sisko orders weapons locked on the enemy ships, he receives a vision from the Bajoran Prophets, who are upset that he intends to sacrifice himself before fulfilling their purposes. Sisko pleads with the aliens to help the Bajoran people, who created a religion around them. The Prophets cause the Dominion ships to vanish, saving Bajor, but warn Sisko that a penance will be exacted.
When Dukat sees the Defiant exit the wormhole he goes mad with rage. The Defiant fires on the station, which cannot respond due to Rom's sabotage. The Dominion fleet has begun retreating to Cardassian space, and over 200 Federation and Klingon ships are approaching the station. As the Dominion evacuates, Dukat searches for Ziyal, who refuses to evacuate with him, admitting that she helped Kira and her friends escape. Dukat is stunned, but forgives his daughter. As Ziyal leaves she is shot by Damar, who heard her confession and executed her as an enemy of the state. Dukat sinks to the floor in grief as Damar leaves the station.
Sisko and company arrive on the Promenade, where Sisko is reunited with Jake. Garak learns of Ziyal's death; the two had grown close prior to the war. Dukat is in a holding cell, sobbing over the loss of his daughter. As he is escorted to the infirmary, he returns Captain Sisko's baseball.