It's been five weeks since Cardassia has joined the Dominion, and for those five weeks, the Dominion has been sending convoys of ships to Cardassian space. The senior staff are viewing the convoy as it passes Deep Space Nine but are aware that war horns are on the horizon and that the Cardassians may want to retake the station. This is reinforced when Dax, Odo, and Kira discover that Quark has smuggled in several crates of Yamok sauce in anticipation of the takeover. Dax orders Odo to dispose of the sauce. Things get worse when Sisko finds out that the Romulans have signed a non-aggression pact with the Dominion. With this recent news, Starfleet has declared that the Dominion convoys must stop, and orders a minefield deployed. The Senior staff are well aware of the consequences of this: that the Dominion in the Alpha Quadrant will see this as a declaration of war, but at this point, Starfleet has no choice.
Rom is able to come up with a design that allows for self replicating mines that are cloaked. But there is a drawback to this approach: the minefield must fully be in place before it can be activated. The Dominion become almost instantly aware of the minefield being deployed. Their ambassador, Weyoun, arrives at Deep Space Nine to issue an ultimatum to stop the deployment of the minefield. After a few rounds of doublespeak about assistance to the poor Cardassian people, both parties know that negotiations are meaningless and that the Dominion will attack Deep Space Nine.
However, Starfleet informs Sisko that no additional forces will be deployed to assist Deep Space Nine with the deployment of the minefield. Sisko asks Martok to take his Bird of Prey to monitor for activity at the Cardassian Border, and report back when the Cardassians and the Dominion start moving. Sisko also asks Kira to call for a meeting of Bajor's leaders, to use his influence as Emissary to have Bajor sign the offer of non-aggression from the Dominion. As Sisko puts it, this is why Sisko stopped Bajor from joining the Federation: if Deep Space Nine were to fall to the Cardassians, Bajor would be an easy target, and why they need to be kept out of the fighting.
Sisko marries Rom and Leeta and Leeta leaves the station with all Bajorans (with the exception of Kira). Sisko also prepares a special computer program to be used if the Federation is to abandon the station. Martok then contacts the station and informs them a large Dominion fleet is on the way. As the station prepares for battle, Garak tells Odo that when the Klingons attacked Deep Space Nine, he and Dukat fought side-by-side against the Klingons and how, for a moment, he considered shooting Dukat In the Back. He only let Dukat live because otherwise he would likely have been dead himself, and that the entire Alpha Quadrant will soon regret his decision.
The Dominion attacks the station and suffers serious casualties. Weyoun is shocked that Deep Space Nine appears to be holding up very well, not realizing that the Federation has been working on countering Dominion weapons ever since the destruction of the U.S.S. Odyssey. Undeterred, Dukat continues to press the attack and soon the shields of Deep Space Nine fall. But this victory comes at a cost: with the Rotarran providing cover fire for the Defiant, Dax is able to successfully deploy the minefield. With this critical objective completed, Sisko declares that there is nothing more to do and orders all Starfleet personnel to evacuate the station.
Sisko makes a speech to the station population and tells them that despite this loss, Sisko is committed to returning to Deep Space Nine. Not only that, while the Dominion and Cardassians were busy retaking the station, a joint Federation and Klingon attack force were able to destroy a critical Dominion shipyard. Sisko then beams off the station to the Defiant, where Garak joins the crew, noting that he is a dead man if he remained on Deep Space Nine. As soon as Sisko is on board, Kira orders the execution of the program Sisko prepared. This program overloads almost all computer systems on Deep Space Nine, leaving the station less then functional, and forcing the Dominion to repair the station if they want to keep it.
At this point, both the Defiant and the Rotarran hightail it from Deep Space Nine, thus completing the conquest of the station by the Dominion. Weyoun finds this victory hollow: the minefield is up, many ships were destroyed in the retaking of this station, and the destruction of the shipyard leaves a poor taste in the Vorta's mouth. Damar and Dukat seem to ignore that development as they almost want to proceed with attacking Bajor until Weyoun says that such an attack is off limits. On the station, the welcoming party consists of Kira, Quark, and Odo. Weyoun is honoured to treat Odo as one of the founders. Meanwhile, Quark finds that Rom did not leave with the Defiant as he is now acting as a spy for the Federation, under the guise of working for his brother. They also discover that Jake also did not leave with the Defiant, an action that infuriates Sisko but leaves him no choice but to leave his son behind.
Dukat escorts Weyoun to Ops where they note the damage done by Sisko's program. Dukat knows this was deliberate, after all, the Cardassians did the same thing when they abandoned the now-rechristened Terok Nor. They walk into Dukat's new office where something catches Weyoun's eye: Sisko's baseball.
- Weyoun: What is that?
Dukat: A message from Sisko.
Weyoun: I don't understand.
Dukat: He's letting me know he'll be back.
The Defiant and Rotarran meet up with a large Federation and Klingon Fleet, ready to take the fight to the Dominion.
The Dominion War has begun.
- Aw, Look! They Really Do Love Each Other: After berating Rom for sending his wife away but staying behind, Quark kisses him on the head while he works to ready the defense grid.
- Big Badass Battle Sequence: An appropriate way to start a war.
- Breaking the Fellowship: The main characters are separated into two groups: those who are forced to leave Deep Space Nine (Captain Sisko, Dax, Worf, O'Brien, Bashir, Nog, Garak), and those who stay behind on the station (Kira, Odo, Quark, Rom, Jake Sisko). And even among those leaving, Worf goes with Martok, away from everyone else.
- Brick Joke: Dax, Kira, and Odo are checking several crates in a cargo bay. Turns out Quark smuggled in several thousand wrappages of Yamok sauce, a Cardassian condiment, in anticipation of the station falling into Cardassian hands. Dax orders the shipment to be dumped. At the end of the episode, when the Dominion and Cardassians retake the station, Quark is wondering where his yamok sauce went.
- Garak recalls the time he and Dukat fought side-by-side against the Klingons and how, for a moment, he considered shooting Dukat In the Back.
- Sisko orders that Deep Space Nine be disabled before being taken by the Dominion, similar to how the Cardassians had the station crippled before Starfleet took it in the pilot episode "Emissary".
- Sisko pushing for Bajor to sign a non-aggression pact is an outgrowth from his prediction in "Rapture".
- Sisko leaves his baseball behind in his office as a message that he'll be back, just as he did in the second season's "The Siege".
- Back in season 1, shortly after the Cardassians withdrew from DS9, Quark found himself with extra yamok sauce he couldn't unload; now as the Cardassians prepare to retake the station he orders a new shipment of the stuff.
- Chekhov's Gun: Program Sisko-197.
- Comically Missing the Point: When Leeta complains about a possible wedding outfit being "two handkerchiefs and a loincloth," Rom suggests losing the handkerchiefs.
- Continuity Nod:
- In a previous episode, Sisko had a vision that told him that if Bajor joined the Federation, Bajor would be destroyed. This episode shows why; here, an independent Bajor signs a non-aggression pact with the Dominion to protect itself, something that could never have happened if Bajor was a Federation world.
- Kira mentions that she learned that Odo has feelings for her a month ago. "Children of Time" aired the previous month.
- Cut Phone Lines: Odo asks Kira to terminate subspace communications from the station in order to prevent security breaches.
- Darkest Hour: Between numerous Dominion warships passing through the wormhole and the Romulans signing a non-aggression pact, Sisko believes they have to act now before it's too late.
- Deal with the Devil:
- Worf's reaction to the Romulans signing a non-aggression pact with the Dominion.
- Sisko uses his status as Emissary and Starfleet Captain to convince the Bajoran government to sign the non-aggression pact with the Dominion, as it is the only way Bajor can escape the coming war.
- Delaying Action: The point of the battle is to buy the Defiant enough time to lay the Space Mines, as well as to draw the Dominion fleet away from a combined Federation / Klingon attack on one of their shipyards. Once that's done, Sisko orders a Tactical Withdrawal.
- The Dreaded: The Teaser rattles off several powers who would rather sign non-aggression pacts than risk a Dominion invasion.
- Sisko leaves his baseball in his office as a message that he'll be back.
- When asked about the possibility of reinforcements, Sisko says that Starfleet's attention is needed elsewhere. Later, before leaving, Sisko reports that Starfleet and Klingon ships destroyed shipyards at Torros III while the Dominion was attacking the station.
- Gunship Rescue: Who says there's never a Klingon around when you need one?
- Heroic Vow: Sisko's final message to those he's leaving behind:"Your sacrifices, our sacrifices, made this victory possible, but no victory can make this moment any easier for me. And I promise, I will not rest until I stand with you again... here... in this place where I belong."
- I Choose to Stay: Jake stays on DS9 (or, as Dukat calls it, Terok Nor) to carry out his reporting duties, reasoning that his relationship to the Emissary gives him a chance as the Dominion won't want to risk alienating the Bajorans. Sisko is not happy.
- I Know You Know I Know: Sisko is well aware that the brief "negotiation" after his refusal to remove the mines is completely meaningless, and that the Dominion are going to attack the station. The only question is whether or not Weyoun realizes that Sisko knows.
- Lock-and-Load Montage: The middle of the episode is taken up by battle preparations, closing with the activation of Deep Space 9's weapons arrays as the Dominion fleet approaches.
- It's a Long Story: Kira tries using this to avoid explaining to Dax why she and Odo are so awkward around each other, but Dax makes her explain.
- Loophole Abuse: Dukat tries getting around the non-aggression pact by stating it was signed by the Dominion, not Cardassia. Weyoun quickly yanks the leash a little by reminding him Cardassia is part of the Dominion now. And Bajor is off limits.
- Nice Job Breaking It, Hero!: Garak accuses himself of this, having spared Dukat from being shot In the Back by the former when the Klingons had previously attacked the station. Now that Dukat is the leader of the Cardassian people, the entire Alpha Quadrant is about to regret Garak's decision.
- Nothing Is the Same Anymore: After three seasons of anticipation, the Federation is now officially at war with the Dominion. Bajor is forced to sign a non-aggression treaty with them, and Federation troops withdraw from Deep Space Nine. At the end of the episode, the Cardassian/Dominion army boards the space station, and it once again becomes Terok Nor, lead by Gul Dukat.
- OOC Is Serious Business: When Weyoun arrives to try and get the minefield taken down, he's dead serious. No fake smiles or compliments. Just a straight threat.
- Pet the Dog: Weyoun is dead serious about Bajor's non-aggression pact with the Dominion, sternly warning Dukat that he expects Cardassia to honor it. Although this probably isn't because he particularly cares about Bajor. If the Dominion breaks its non-aggression pact with Bajor, then the other major powers that it has similar pacts with will know the Dominion isn't to be trusted and could be induced to side with the Federation. Weyoun is angling to protect the Dominion, nothing more.
- Pyrrhic Victory: Gul Dukat successfully retakes the station, but fails to stop the minefield from being activated while a Dominion shipyard is destroyed elsewhere. Weyoun also notes that 50 ships were destroyed in their effort to take the station.
- Relationship Upgrade: Odo tells Kira that he's been thinking about this, but he's decided not to during the current crisis.
- Salt the Earth: Kira executes Sisko's program to disable the station once Starfleet has left. Justified, as it denies the Dominion any intelligence it could've obtained from the Federation computers (and lets Sisko and Kira flip the bird to Dukat).
- Scotty Time: Dax and O'Brien repeatedly say they need more time to lay the minefield. Naturally, they get the job done.
- Shout-Out: Rom's speech to Leeta about getting her off the station is a reference to Casablanca.
- Spell My Name with an "S": Bashir tells Jake that his name is spelled with an "I".
- Stock Footage: A lot of the shots of DS9 readying and firing weapons are reused from "The Way of the Warrior", with the Klingon ships replaced with Cardassian and Dominion ones.
- Technology Marches On: In-Universe. After capturing a Jem'Hadar fighter, Starfleet was finally able to adjust their shields to protect against Dominion weapons.
- Teeth-Clenched Teamwork: Dukat clearly wants to try to use the Dominion to his own ends and thinks he's only putting up with them as long as it takes to make Cardassia great again, meaning defeating and destroying the Federation and Klingons and retaking Bajor. The Dominion, in the person of Weyoun, has other ideas and sternly informs him that he will honor the non-aggression pact. Dukat grudgingly agrees, with an unspoken "for now" evident in his tone and the glance he gives to Damar.
- That Came Out Wrong: Rom asking Sisko to perform his and Leeta's wedding:"Will you marry me? I mean, us? I mean...will you perform our wedding?"
- This Explains So Much: Played for Laughs when Kira admits to Jadzia that Odo has a crush on her.Jadzia: That explains a lot.
Kira: What do you mean?
Jadzia: ... I don't know, really. It just seemed like the thing to say.
- Underestimating Badassery: Federation shields had always proven useless against Dominion weapons, but that's not the case anymore. Weyoun is stunned. Justified thanks to the fact the Federation had been handed a Jem'Hadar fighter nearly intact by another Vorta in "The Ship".
- We Will Meet Again: Sisko left his baseball behind in his office.Weyoun: What is that?
Dukat: A message from Sisko.
Weyoun: I don't understand.
Dukat: He's letting me know he'll be back.
- Wham Episode: After three years of waiting, the Alpha Quadrant is finally at war between the Dominion and Cardassia against the Federation-Klingon Alliance.
- Wham Shot: The final shot of the episode shows the Defiant and Martok's Bird-Of-Prey flying off into space...where they meet with what looks like the entire combined fleets of both the Federation and the Klingon Empire! The instant you see this, you know just how serious things have gotten!