Jake is working on a science project, the only means of learning on DS9, about plants and what kinds of water yield the best results. Sisko asks him if he could do any project at all, Jake gives him an honest answer (after learning that flying a runabout is not a science project): visit the Gamma Quadrant. With the need to do actual science being a planetary survey, it will be a working vacation for them. However, just as Sisko is delegating his station duties, Jake says that Nog will be coming along as he needs to get a good grade as well. Meanwhile, Quark learns that the senior staff has rejected his proposal for advertising, as he's only a greedy merchant and advertising clearly won't improve the station economy. So, he invites himself along on the trip.The group arrives at an uninhabited planet, which Quark mentions he wants to start exploiting for resources. They do some farting about and there's whacky antics with Quark, causing Nog to run off and Jake to go after him. Just as it looks like Sisko is going to beat the crap out of Quark for being an annoyance, a woman stumbles out of the forest. She says she's running from the Jem'Hadar, who then appear out of thin air and take the three captive. The kids return to find their guardians gone, and decide to follow the footprints. In a cave, the woman introduces herself as Eris, who fills them in on the Jem'Hadar: they're the feared soldiers of the Dominion. Her homeworld was offered membership, but when they refused, the Dominion sent in the Jem'Hadar which quickly conquered them. Despite this, Sisko begins working on an escape plan. Eris has psionic powers, but they are being suppressed with a collar she's wearing.Jake and Nog find the cave, being guarded by tall reptilians. One of the Jem'Hadar finally comes speak with Sisko and is blunt: the Dominion will not tolerate Starfleet boldly going through their territory. The kids meanwhile beam up to the runabout to try and get help, but unfortunately they don't know how to disengage the autopilot or the access code to set a new course. A ship leaves the planet and arrives at DS9. The Jem'Hadar inform the senior staff that Sisko is being detained for questioning, and delivers a list of ships that have been destroyed for violating Dominion space...on a padd from a Bajoran colony in the Gamma Quadrant. Shortly afterwards, the USS Odyssey arrives, a Galaxy-class starship captained by an older, white-haired, balding captain, and they begin planning a rescue mission.Arriving in the Gamma Quadrant, they find the runabout with Jake and Nog, and O'Brien beams over to help fix the shuttle. Meanwhile, Quark removes Eris' collar and they make their escape. In space, three Jem'Hadar attack fighters engage the Odyssey and the DS9 runabouts. The Dominion's weapons effortlessly pass through the Starfleet shields and the Odyssey is quickly disabled. Sisko, Quark, and Eris are rescued, but while they make a run for it, one of the fighters slams into the Odyssey, destroying it. Back in the Alpha Quadrant, Quark realizes that Eris' collar has nothing in it. They try to apprehend her, but she beams away, telling them that they have no idea what's begun...
- Badass Boast: Faced with a new threat from the Gamma Quadrant, Sisko ends the season with one."If the Dominion comes through the wormhole, the first battle will be fought here, and I intend to be ready for them."
- Black Box: Subverted; Eris and company clearly expected the prisoners to simply accept the "psychic inhibitor" collar as stated when she used powers after having it removed; it really has no working parts other than the lock. This actually works on the humans, but then Quark tries to reverse engineer the "technology" for a quick profit...
- Blatant Lies: Quark says that his brother Rom is not quite as liberal as he is when it comes to parenting...even though Quark is extremely strict on everything... Not to mention that we've seen Rom is unimaginably liberal by Ferengi standards.
- Brick Joke: Suddenly, that runabout lesson for Jake sounds very useful, Sisko.
- Call Back: Quark tries selling his captors 1000 cases of Tulaberry wine.
- Curb-Stomp Battle / The Worf Effect: The Odyssey, a Galaxy-class starship like the Enterprise-D on TNG, is utterly decimated and destroyed by the Jem'Hadar.
- Early Installment Weirdness: The Jem'Hadar guard doesn't have a visible Ketracel-White tube.
- Eris' telekinetic powers are never seen with any other Vorta. Word of God says that she alone was given these powers by the Founders.
- Eris escapes by having herself beamed out. The Dominion is otherwise never seen using cloaking technology, so how she did so is a mystery. The creative staff said that she was supposed to return but the actress wasn't available, so it isn't just a suicide. In addition, later episodes would show that the Dominion's transporter technology is far more advanced with a range extending to several lightyears.
- Expy: Captain Keogh and the Odyssey are intentional ones for Captain Picard and the Enterprise to show just how dangerous the Dominion are. Word of God says that the Enterprise would have fared the same.
- False Innocence Trick: Eris claims that her people were conquered by the Dominion. It turns out that they're actually second-in-command after the Founders.
- Informed Attribute: Captain Keogh's supposedly extremely arrogant, but the entire time on screen he's shown to be cautious and reasonable. He always takes advice and never underestimates the Jem'Hadar's abilities.
- It Has Only Just Begun: Eris' parting words to Sisko: "You have no idea what's begun here."
- Knight of Cerebus: This show was always Darker and Edgier than its predecessors, but the introduction of the Dominion makes it even more so.
- The Mole / Trojan Horse: Eris turns out to be a Dominion spy who's pretending to be a fugitive from them, so that she would be taken to Deep Space Nine. She's discovered before she manages to do any damage, though.
- Meaningful Name: In Greek mythology, Eris is the goddess of discord.
- Never Trust a Trailer: Deliberately invoked by the crew, as the destruction of the Odyssey was played up as the Enterprise in the previews. Even with the TNG crew still safe and sound, the Dominion being able to take down a ship just like it speaks volumes about how powerful they are.
- Nothing Is the Same Anymore: The crew finally meets this mysterious Dominion, and learn in no uncertain terms that they are not allowed to explore through their territory. And the Dominion draws the first blood by destroying the Odyssey.
- Oh, Crap!: Nog is visibly soiling himself when the runabout computer indicates that there's an incoming ship."Computer, evasive maneuvers! Launch torpedoes! And escape pods!"
- One Riot, One Ranger: Deconstructed. The Odyssey being a Galaxy-class ship like the Enterprise, it's expected that she'll be able to rescue Sisko and Quark with no trouble and the Jem'Hadar will simply be a Monster of the Week. Instead, the Odyssey is effortlessly destroyed and the Jem'Hadar go on to be a major arc villain for the entire series. Tellingly, from this point forward Starfleet begins to operate in fleet-sized groups whenever dealing with the Dominion.
- Pint-Sized Powerhouse: The Jem'Hadar fighters. The Odyssey is no match for them, especially since her Deflector Shields can't block Dominion weapons.
- Ramming Always Works: How the Jem'Hadar destroy the Odyssey, just to prove that they're serious.
- Reasonable Authority Figure: Captain Keogh. He's hesitant to allow the DS9 crew to accompany the Odyssey on the mission to rescue Sisko and Quark because he doesn't like putting inexperienced people in the line of fire.
- "The Reason You Suck" Speech: Quark of all people gives Sisko a verbal bitch-smacking.Quark: The way I see it, hew-mons used to be a lot like Ferengi: greedy, acquisitive, interested only in profit. We're a constant reminder of a part of your past you'd like to forget.
Sisko: We don't have time for this...
Quark: But you're overlooking something: Hew-mons used to be a lot worse than the Ferengi. Slavery. Concentration camps. Interstellar wars. We have nothing in our past that approaches that kind of barbarism. You see? We're nothing like you. We're better.
- Of course, the Ferengi treat their women as second-class citizens. On the other hand, "Hew-Mon" society has done some pretty awful things to women as well... some far worse than anything seen on Ferenginar.
- Shout-Out: When Nog and Jake can't find Sisko and Quark, Nog suggests that they were attacked by a wild animal. Jake points out that the only surface-dwelling animals on the planet are insects. "Maybe they were attacked by a ferocious tree."
- Spanner in the Works: Quark's greed and interest in telepathic-dampening technology led him to keep the collar Eris wore. When he scanned it, it led him to realize it didn't have the technology to do as it was supposed to. He promptly told Sisko and that stopped Eris cold.
- Wham Episode: We finally get to meet members of The Dominion, the Gamma Quadrant power which has been alluded to in several episodes during season 2. Turns out they are not happy with the Federation exploring the Gamma Quadrant, and they threaten to go to war against them if this continues. To back their threats up they demonstrate their superior military technology in various ways, culminating with the destruction of a Galaxy-class starship.Mark Oshiro: Remember when the Cardassians were the major threat to peace in this world? Remember when they were the main antagonist? DO YOU REMEMBER THIS TIME? Because in just one episode, Deep Space Nine has upended everything, giving us a new villain thatís not even one person, nor is it one species, NOR DO THEY SEEM TO HAVE A SINGLE DISCERNIBLE WEAKNESS, EITHER. After teasing us with mentions of the Dominion for two seasons, the writers barge into our room, they punch us right in the heart, and then they dart away, laughing the whole time. The Dominion are here, and they are not gonna fuck around.
- You Have No Idea Who You're Dealing With: See It Has Only Just Begun above.