The previous episode marked the first occasion that anyone from the Alpha Quadrant had met the Jem'Hadar and lived to tell the tale, as the Dominion made a very blunt demonstration of their intentions - chiefly by destroying a Galaxy-class starship making its way out of the Gamma Quadrant.
This episode starts with Major Kira leading a discussion in Ops about how best to prepare should the Dominion launch an attack through the wormhole. While the team comes to the depressing conclusion that Deep Space Nine could only hope to resist being taken over for at best two hours, an unusual starship decloaks 300m from the docking ring. Commander Sisko has returned from Earth in the newly recommissioned USS Defiant.
The Commander tells the crew all about the new ship in the conference room. An overpowered prototype originally designed to combat the Borg, the Defiant has been brought out of the warehouse and fitted with a Romulan cloaking device. Sisko introduces two new officers: a Romulan sub-commander, there to supervise the proper use of the cloaking device, and a Lieutenant Commander Michael Eddington, from Starfleet Security. Odo is immediately suspicious of the high ranking security officer. As the briefing concludes he confronts Sisko and after an antagonistic conversation promises Sisko his resignation as Head of Station Security within the hour.
The entire command crew, including Doctor Bashir, Chief O'Brien and Lieutenant Dax, as well as Odo and Quark (but curiously not Lt Cdr Eddington) set out in the Defiant the next morning on a mission to find the Founders, leaders of the Dominion, to establish peaceful terms for the Federation's exploration of the Gamma Quadrant. During this mission, Odo develops an apparently inexplicable fascination with the Omarion Nebula. The crew are at first successful with the new cloaking device in evading Dominion patrols, although Jem'Hadar vessels seem capable of detecting something while the Defiant travels at warp speed.
The investigations of the crew lead them to an isolated and apparently undefended communications relay. Chief O'Brien and Lt Dax are sent on an away mission to learn what they can from the relay's memory banks. As they transmit coordinates of where the relay station sends on 80% of its communications traffic, the pair are assaulted and communications jammed. With three Jem'Hadar ships also on course to intercept, Commander Sisko makes the hard decision to keep the Defiant cloaked and leave his two officers to their fate.
While the crew adjust to this loss, and as Odo's obsession with the Omarion Nebula deepens, a Jem'Hadar patrol manages to detect the Defiant through its cloak, and launch an attack. The crew manage to destroy one of the Dominion vessels before main power is forced offline and the Defiant loses shields. Dozens of Jem'Hadar troops then board the ship. In the ensuing combat, the Romulan Sub-commander is knocked unconscious and Major Kira apparently shot by a Jem'Hadar beam weapon.
Odo rescues Kira, escaping in a small shuttlecraft. Cinematographically, the audience learns of this at the same time Kira does: Kira was unconscious, and when Odo informs her of the escape when she awakens, he is in effect informing the audience, as well. During the same scene, Odo informs Kira that they are currently en route to the Omarion Nebula. She is dismayed, claiming she did not consent to being placed in her current situation, and arguing that they should have headed straight back to the Alpha Quadrant. Using the vessel's sensors, Kira detects a rogue class-M planet. Odo resolves to land on the planet. There, Odo and Kira encounter an apparent lake of shapeshifters, as a group of them solidify and welcome Odo home.