Following a recap of the last part, we open where we left off: with Odo meeting his people, the Changelings, for the first time. The female Changeling is thrilled to see him, and upon briefly linking with him, he realizes that he is indeed home.
Having been adrift in a shuttlecraft for six days while trying to reach the wormhole, Sisko and Bashir remained worried about the fate of the rest of the crew when they're suddenly rescued by O'Brien and Dax. While other ships continue to search for the remaining crew, they set course for the station, where a big surprise awaits them.
Odo has been kept waiting by his people and is growing impatient as they deliberate in the Great Link about his arrival. Finally, the female Changeling re-emerges and begins taking Odo under her wing. She warns Kira that they can't allow her to send a signal, as they value their privacy, and explains to Odo their people's distrust of "solids". Kira sneaks off to try to get a masked signal off anyway.
Arriving on the station, Sisko is greeted by Admiral Nechayev, who informs him that representatives of the Dominion have already arrived and are eager to meet him. Sisko meets the lead representative, a Vorta named Borath. Sisko notes the resemblance to Eris, and Borath reveals that he is one of the Founders. He is here to establish a treaty between the Dominion and the Federation.
On the Promenade, Garak surprises Bashir by revealing that the Cardassian Central Command is in favor of the treaty talks, but he himself has misgivings. They encounter Subcommander T'Rul, who is upset that the Romulans have been left out of the talks. Meanwhile, back on the Changeling homeworld, Kira finds that there's too much interference to send any kind of signal, so she meets up with Odo again. As he's been practicing his shapeshifting, he realizes it's time to regenerate, and is thus forced to leave a frustrated Kira on her own. Back on DS9, Sisko is distressed about the Romulans being left out, but Nechayev tells him that if the Federation-Dominion alliance happens, the Romulan Star Empire will become irrelevant.
Odo continues to learn about his people from the female Changeling, explaining their distrust of monoform species by telling him how they have been hunted and persecuted by solids for ages. The two link again, as Kira is off investigating a strange door on another part of the surface. She finds this strange since Changelings wouldn't seem to have a need for doors, but attempts to scan through the door are stymied because of the mysterious interference field.
A Jem'Hadar soldier picks a fight with O'Brien at Quark's, and Bashir is angered when the soldier is allowed to go free. Eddington points out that for now, they have to put up with the Jem'Hadar and advises giving them a wide berth. The bad news mounts for Sisko as Dax informs him she's being transferred off the station. Incensed by recent developments, Sisko demands answers from Nechayev, who informs him that responsibility for Bajor is being turned over to the Dominion, though Sisko will be promoted to captain for his efforts. Neither this nor Borath's assurances that Bajor will fall in line will placate him, especially since Sisko realizes that if Bajor doesn't willingly comply with these terms, the Jem'Hadar will ensure that they do. And to make matters even worse, it's already a done deal - the treaty has already been signed.
Odo is thrilled to be exploring new forms and what it means to be these forms, but Kira brings her concern about the door to him. Odo confirms that his people wouldn't need a door since they don't even like to take solid form if they don't have to, so he agrees to help Kira investigate it. Back on the station, Garak reveals to Sisko that the Bajorans have just allied with the Romulans, coming to the conclusion that their leaders have all gone insane. As the two discuss the situation, T'Rul shows up, being pursued by two Jem'Hadar soldiers, but before she can reach Sisko she is gunned down. Sisko retaliates but is beaten down and arrested.
Garak, Dax, and Bashir proceed to bust Sisko out of security, while O'Brien readies the Rio Grande with a compliment of torpedoes. Dax has come to the same conclusion as Sisko: the only way to stop the Dominion is to collapse the wormhole. Meanwhile, Odo realizes that the mysterious door isn't meant to keep anyone out, but to keep whatever's inside in, and the lock is designed to only be opened by a Changeling without the use of special tools or weapons. Back on the station, Sisko and the others fight their way to the runabout, although Garak is killed in the process. The Rio Grande launches, and they're hailed by Nechayev and Borath, who order them to stand down, but Sisko refuses, and gives the order to fire. The wormhole briefly opens before the torpedoes detonate, imploding the passage...
Odo shapeshifts his arm to open the door, and he and Kira find two Jem'Hadar waiting behind it. They take them into an underground chamber, where they find Sisko, Dax, Bashir, O'Brien, and T'Rul unconscious on inclined tables, and Borath and two Vorta technicians standing watch over them. Borath reveals that they have been running a simulation, to gauge their reactions to the Dominion gaining a foothold in the Alpha Quadrant. Borath isn't happy with their stubbornness, but thankful that he's not the one who has to deal with that problem. But the female Changeling arrives and points out that she does. Kira realizes the Changelings are part of the Dominion, but she is corrected: they are the Dominion. Specifically, they're the Founders.
Once, the Changelings explored the galaxy, but their persecution led to their creation of the Dominion. Now, the hunted dominate those who would hunt them. Their only concern is the protection of their own. Odo is unable to reconcile their philosophy with his sense of justice, but she attempts to convince him that it's order, not justice, that he really seeks. He refuses to stay with them, though, and insists on taking the others. As no Changeling has ever harmed another, she agrees to let them go, despite Borath's objections. Sisko and the others beam up to the orbiting Defiant, but Kira stays behind with Odo as he bids his farewell. The female Changeling remains hopeful that Odo will take his rightful place in the Great Link someday; as she reenters the Link herself, Odo and Kira transport away.
- All Just a Dream: The events on Deep Space Nine turn out to be a simulation the Dominion runs inside the minds of the captured protagonists. Most viewers will probably guess this plot twist by the time the popular supporting character Garak is casually killed.
- Appropriated Appellation: The term "Changeling" used to be a slur against shape-shifters, until the Founders took it as their own.
- Artistic License Astronomy: In the previous episode, the Changelings' homeworld was said to be a rogue planet, a planet that doesn't orbit a star. But the planet seems to have a constant source of illumination, equivalent to the level of light during a full moon on Earth. And in this episode we see the source of that light is a nearby star. So if the planet is close enough to the star that the star illuminates it so much, it should also be on the star's orbit.
- Attack Pattern Theta: Used to torpedo the wormhole.
- Could Say It, But...: At one point, Garak sits down with Sisko at the Replimat and the two compare notes, suggesting that their leaders have gone insane for allying with the Dominion. Garak points out that there's nothing either of them can do officially to stop the Dominion takeover. Sisko agrees that they can't officially do anything about it...and that ''is'' a pity.
- Early Installment Weirdness:
- The Changelings are significantly more bronze than they would be in later appearances.
- The real Borath is much ruder to Odo than later Vorta would ever dare to be to a Changeling, whether he was a Founder or not.
- Famous Last Words:Garak: Doctor, I'm afraid I won't be able to have lunch with you today.
- Subverted, though, as it was only an illusion of Garak that was killed.
- Fantastic Racism: The female changeling tells Odo about how her people were persecuted and killed by other races, which is why they now live in isolation.
- I Am the Noun: Delivered as one hell of a Wham Line:Kira: You belong to the Dominion, don't you?Female Changeling: Belong to it? Major, the Changelings are the Dominion.
- In the Back: How T'Rul is shot.
- Indy Ploy: Waylaid by a Jem'Hadar patrol, Garak pretends to turn traitor on the others and then shoots the Jem'Hadar while their guards are down.
- Instant Sedation: Garak uses the off-button hypospray on Eddington while breaking Sisko out of the brig.
- Karma Houdini: One of many things that Sisko is pissed about—a Jem'Hadar beats up O'Brien and isn't punished for it.
- No Changeling Has Ever Harmed Another: This is why the female changeling just lets Odo and the others go.
- O.O.C. Is Serious Business: Nechayev's behavior. The fact that the admiral who played hardass with the Cardassians on TNG, and even ordered Captain Picard to wipe out the entire Borg Collective if given the chance, is willing to give in to all the Dominion's demands without protest is a clear sign to Sisko that something is very wrong.
- The Quisling: Simulation!Nechayev bargains away control of the wormhole, Deep Space Nine, and Bajor itself in exchange for 'friendship' with the newly-arrived Dominion. Sisko tells her point-blank how stupid it is to give the Dominion a free foothold in the Alpha Quadrant while simultaneously pissing off the Bajorans and Romulans in the process, but she is unconcerned.
- The Reveal: The Changelings are the Founders of the Dominion.
- Screw the Rules, I'm Doing What's Right!: Sisko, Dax, O'Brien, Bashir, and Garak go rogue to collapse the wormhole to keep the Dominion away from the Alpha Quadrant.
- To Be Lawful or Good: A variation; Odo parts ways with the other changelings when he realizes that they're only "lawful" without the "good" part.
- Trojan Prisoner: Garak pulls this trick on the Jem'Hadar.
- Wham Episode: Odo has discovered the other members of his race, and he finally feels like he belongs somewhere... But then it turns out the Changelings are the secret leaders of the Dominion, and Odo has no choice but to reject them in disgust. Also, it's made clear that peaceful co-existence with the Dominion is highly unlikely, so the Federation and its allies will have to prepare for war.