The crew of DS9 eagerly await Commander Sisko's return from Earth while discussing the threat of the Dominion when they get a sudden surprise: a Federation starship decloaking just off the station! Sisko reveals that this is his baby: the USS Defiant, a prototype of what is officially dubbed an "escort", but is essentially a weapons platform with warp engines. He had designed it to fight the Borg, but it was overpowered and unreliable, and mothballed when the Borg threat became less urgent. With the new threat of the Dominion, however, he's had it commissioned, and instructs Chief O'Brien to help work out the kinks. Its cloaking device is on loan from the Romulans, who have agreed to its use only in the Gamma Quadrant (aside from the stunt arriving at the station) in exchange for all intelligence they gather on the Dominion. And their first mission is to track down the homeworld of the Dominion's mysterious Founders.
Joining the crew for this mission are Subcommander T'Rul, the Romulan representative who will be responsible for the cloak, and Lt. Commander Michael Eddington, a new Starfleet security officer. Odo chafes at the idea of having Starfleet oversight on his job, and prepares to resign. Kira meets with Odo in private and tells him the Bajoran government has requested his presence on the mission, a claim Odo doesn't exactly believe, but Kira convinces him to participate anyway, since this would be a good opportunity to see if they can find more clues about his people. In the meantime, Sisko orders Quark to join the mission as well at the request of Grand Nagus Zek, due to Quark's experience negotiating with members of the Dominion. As the ship prepares to leave, Odo arrives to join up, but is less than thrilled to be stuck sharing quarters with Quark.
The Defiant apparently succeeds in eluding an anti-proton scan from a Jem'Hadar warship, and proceeds to the Karemma homeworld, where Quark makes inquiries about the Founders. The Karemman minister reveals that all contact with Dominion leadership is handled through a race called the Vorta, and he's reluctant to help them further. Sisko points out that not helping them could threaten the Karemma's trade alliance with the Ferengi, which could potentially upset the Founders, so the minister directs them to an unmanned relay station in the Callinon system. While studying the star chart, Odo is drawn to the Omarion Nebula, which is somehow familiar to him. Having fulfilled his duty to Sisko, Quark opts to stay behind to continue trade relations with the Karemma.
The Defiant reaches the relay station, but the crew finds it's a trap; Dax and O'Brien are stranded, and the ship is forced to evade the Jem'Hadar again, barely escaping. Odo in the meanwhile confesses his need to seek out the Omarion Nebula, but for the moment the mission comes first. The ship comes under fire as the Jem'Hadar have penetrated the cloak, and the Defiant is battered and boarded. Kira is knocked out, but Odo is able to rescue her and escape in a shuttlepod. When she comes to, she is chagrined to find that Odo is heading to the nebula instead of the wormhole, but it's too late to complain. Inside the nebula, they land on a rogue planet mostly covered by a familiar-looking fluid. Several humanoid forms who take on an appearance similar to Odo's emerge from the amber ocean; one of these Changelings, taking a female shape, addresses Odo:
- "Welcome home."
- Abandon Ship: Sisko calls for this, but he and his crew are captured before they can escape. Only Odo and Kira make it off the Defiant.
- Attack Pattern Alpha: Evasive Pattern Delta-5.
- Character Development: Bajor is definitely starting to grow on Sisko, as he gets his personal effects from storage and brings them to the station.
- Continuity Nod: The USS Defiant is named for the ship of the same name in the TOS episode "The Tholian Web". That earlier Defiant would go on to reappear in the Enterprise episode "In a Mirror, Darkly".
- Curbstomp Battle: Once again, the Jem'Hadar have Starfleet's number when it comes to combat. Unlike the previous episode, however, where the USS Odyssey got completely obliterated without so much as scratching any of the Jem'Hadar ships, the Defiant at least manages to destroy one Jem'Hadar ship before being disabled.
- Early Installment Weirdness:
- Odo gets a new uniform, based on Mirror!Odo's outfit from "Crossover." It includes a belt that he would only wear for the next five episodes.
- Sisko, Bashir, and Kira get shot by the Jem'Hadar's weapons. Later seasons would show that the Dominion's weapons do not have a stun setting.
- Enemy Mine: The Federation takes the Dominion threat seriously enough to do a deal with the Romulans, acquiring a cloaking device for the Defiant at the price of having a Romulan observer on board.
- Explosive Instrumentation: Damn near every console on the Defiant blows up during the battle, one of which takes out the Disposable Pilot.
- Flawed Prototype: The Defiant. She nearly flies herself apart because her engines are too powerful, her medical facilities are inadequate by Bashir's standards, and her replicators can't make a decent cup of coffee!
- Got Volunteered: After the events of the last episode, Quark has no interest in returning to the Gamma Quadrant. Unfortunately, Sisko and the Grand Nagus don't give him that option.
- I'm Not Here to Make Friends: T'Rul. Eddington, on the other hand, wants to make friends.
- No One Gets Left Behind: A rare aversion when Sisko is forced to abandon Dax and O'Brien when they're captured by the Jem'Hadar.
- Permission to Speak Freely: Kira, before asking Sisko what the hell Starfleet is thinking by bringing in a new security chief. Sisko agrees with her, but admits that the admirals have valid reasons for not liking Odo.
- See the Invisible: The Jem'Hadar figure out how to spot the Defiant through her Invisibility Cloak and launch a surprise attack.
- Skewed Priorities: Quark suggests Rom accompany Sisko on the mission instead. After all, he just has a son. Quark has a business.
- Staff of Authority: Sisko brings the Grand Nagus' staff with him to help convince Quark to come on the mission.
- Taking A Third Option: This trope is directly quoted by Kira after the senior staff (minus Sisko) has run many simulations and found that the station will be overrun by the Dominion very quickly in the event of a full-scale assault. Dax says that that leaves them with two options abandon the station and make their stand on Bajor, or collapse the entrance to the wormhole. Kira says, "I want a third option" and almost at that very moment, the third option appears in the form of the new USS Defiant.
- Took a Level in Jerkass: Odo is much crankier and meaner than his usual self. Justified in that he has been just effectively demoted from his position as head of station security, which he attributes to discrimination.
- Wham Line: "Welcome home."
- Wham Shot: The Defiant decloaking.O'Brien: A Federation ship...with a cloaking device?
- What a Piece of Junk: The Defiant. Everyone sees her as The Alleged Starship until her trial by fire.
- The Worf Effect: Even the new Super Prototype USS Defiant is still not enough against the Dominion! Somewhat justified, as this was her first outing and Chief O'Brien has a long ways to go to fix all the problems on board.