It's been five weeks since Cardassia has joined the Dominion. Since then, the Dominion has been sending convoys of ships to Cardassian space, clearly in preparation for an invasion. Things get worse when Sisko finds out that the Romulans have signed a non-aggression pact with the Dominion. Starfleet declares that the Dominion convoys must stop and orders a minefield deployed, even though this act will likely spark the war itself.
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 be fully in place before activation. The Dominion become almost instantly aware of the minefield being deployed. Their ambassador, Weyoun, arrives at Deep Space Nine and brokers a deal with Sisko, but afterward, the captain reveals that the negotiations were merely formality, and the Dominion will soon attack Deep Space Nine.
With Starfleet offering no additional forces, it's up to the station to finish the minefield before the attack. 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). Garak also sends Tora Ziyal to Bajor and stays behind, assuring her that he's a survivor. Quark stays behind to protect his bar but urges Rom to save himself. Rom refuses, saying that he's got to protect his brother. As the station crew prepares for war, Sisko creates 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.
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. Kira executes Sisko's program, which overloads almost all computer systems on Deep Space Nine, leaving the station less then functional.
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. Dukat is glowing with victory, though Weyoun is less than impressed by its cost. He forbids Dukat from proceeding with an attack on Bajor, honoring their treaty. On the station, Kira, Quark, and Odo welcome their new invaders on behalf of Bajor. Weyoun is honored to treat Odo as one of the founders. Meanwhile, Rom resumes his duties as Quark's assistant, but now acting as a spy for the Federation. Jake has also stayed behind to report on the war, trusting that his status as the son of the Emissary will protect him, 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. In Dukat's new office, he notices that Sisko has left behind his baseball and realizes that it's a message from Sisko promising to return.
The Defiant and Rotarran meet up with a massive Federation and Klingon fleet. 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.
- Call-Back: Sisko pushing for Bajor to sign a non-aggression pact is an outgrowth from his prediction in "Rapture".
- 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.
- 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 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.
- Jake resumes his duties assisting Bashir during a war while acting as a war correspondent, just as he did earlier in the season in Nor the Battle to the Strong.
- Rom references his Gold Digger ex-wife when getting cold feet over his impending wedding.
- Cut Phone Lines: Odo asks Kira to terminate subspace communications from the station in order to prevent security breaches, though he has dummy transmissions prepared in order to make the Dominion think that itís business as usual.
- 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.
- Dramatic Irony: A Meta cross-series one. "Call to Arms" aired concurrently with the Voyager Season Three finale ''Scorpion'', wherein Janeway and her crew were also dealing with an alien invasion over in the Delta Quadrant. The Deep Space crew is thus fighting to save the Alpha Quadrant from the Dominion while being completely unaware that not only is another invasion happening on the other side of the galaxy, but that the threat posed by Species 8472 is far worse than the threat of the Dominion.
- End of an Era: Meta example. This episode marked the departure of Ira Behr's creative collaborator, Dominion co-architect, and longtime DS9 Staff Writer Robert Hewitt Wolfe from the show. Wolfe would briefly return one more time in the final Season to write ''Field of Fire".
- Foregone Conclusion: In-universe example. When Weyoun confronts Sisko about the minefield, Sisko doesn't bother denying it. He knew the Dominion was going to realize what was happening sooner or later.
- 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.
- Weyoun yanking Dukat's leash when he discusses re-annexing Bajor. After a subtle hint back in "Ties of Blood and Water", it's the first overt confirmation that the Cardassian-Dominion alliance isn't one of equals and discontent's been seeded. This will become very important over the final two Seasons.
- Freeze-Frame Bonus: Among the ships in the massive fleet at the end are two new Defiant-class ships, showing for the first time that the design has gone into production.
- Gallows Humor: Odo and Kira laugh about how putting aside the possibility of a relationship between them to focus on the impending battle makes them feel much less nervous.
- 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 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 by hurting him. Sisko is not happy, but it's not as if he can go back to get him.
- 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.
- O.O.C. 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.
- Pragmatic Villain: Weyoun is dead serious about Bajor's non-aggression pact with the Dominion, sternly warning Dukat that he expects Cardassia to honor it. 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 is jubilant at taking DS9, but Weyoun is quick to point out that it cost them fifty ships and their shipyards to take the station, and that Dukat had failed to prevent the wormhole being mined, cutting them off from further Dominion reinforcements. Even in defeat, Starfleet achieved all of its objectives for the battle.
- 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.
- 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". Starfleet has thus had nearly a year to reverse engineer its technologies and produce countermeasures.
- 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!