While in the Great Link ("Broken Link"), Odo suspected that the Changelings were hiding information from him. What he was able to gleen from the Link allowed him to realize that Klingon Chancellor Gowron is actually a Changeling. Starfleet requests that Sisko reveal Gowron for who he truly is and put an end to the hostile actions of the Klingon Empire.
Stardate 50049.3: While on a mining survey on a planet in the Gamma Quadrant, Sisko and his team witness a Jem'Hadar vessel crash near their location. Examining the wreckage, they find over thirty Jem'Hadar dead. It isn't long before another Jem'Hadar warship arrives and destroys the orbiting Runabout and it's crew. Fortunately for Sisko's team, they were able to radio to Deep Space Nine and call for the Defiant.
Worf sees a Klingon woman arrive at Deep Space Nine and is captivated by her. Unfortunately, the woman has come to see Quark. Grilka ("The House of Quark") returns to DS9 to have Quark assist her in calculating her finances. Elsewhere, Chief O'Brien concentrates on making Major Kira, the holder of his child, as happy as she can be.
Worried about his unborn son's consumption of caffeine, Chief O'Brien tries to ween Major Kira off of her raktajinos. On a more distressing note, Sisko informs the crew that Doctor Bashir and Jake have gone to aid a Federation colony that has been attacked by the Klingons.
Chief O'Brien and Dr. Bashir have over watered Keiko's bonsai trees and are worried about her reaction when she returns from Bajor. Unfortunately, that will be the least of the Chief's worries when Keiko returns with an alien presence controlling her. For Keiko to survive, O'Brien must do exactly what the alien says.
Starfleet Temporal Security questions Captain Sisko over the matter of a time travel incident aboard the Defiant. While returning from Cardassia Prime with a Bajoran Orb, the Defiant suffers a temporary power drain. Once systems come back online, the crew gazes out on the Constitution-class USS Enterprise.
Worf and Jadzia have planned a vacation together. At first, they had planned to go to Earth, but then Worf suggested the vacation planet of Risa. By chance, and much to Worf's chagrin, Dr. Bashir, Leeta, and Quark had the same idea. Making the long trip to Risa, the group arrives just as a moralistic cult begins to express their views with more than just words.
Returning from a Bajoran conference on the Cardassian Occupation, Sisko, Odo, Dax, and Garak pass through a plasma storm and are rendered unconscious. When they awaken, they are on Terok Nor seven years ago when Odo was the security chief. Trouble is, the chief on the station is not Odo. Instead, it is Odo's predecessor and the four DS9 crew are Bajorans.
Cadet Nog returns to Deep Space Nine to begin his field training. To keep him company, Jake moves in with him. Meanwhile, Quark has been accused of a high security crime and is being taken by Odo to the grand jury hearing.
A rare painting depicting the ancient Bajoran city of B'Hala is returned from the Cardassians. Markings on an obelisk in the painting are said to give the exact location of B'Hala and Captain Sisko tries to discover its location. Deciphering the symbols in a holosuite, the Captain suffers a plasma burst from the holosuite's system and begins to see visions.
Members of Major Kira's resistance cell during the Cardassian Occupation are being killed. In each instance, an untracable subspace message is sent to the Major telling her that her friends are dead. Kira tries to contact the rest of her former comrades in order to save their lives.
The time has come for Kira Nerys to give birth to the O'Briens' baby boy. The Bajoran ceremony of birth begins in preparation for the arrival... and stretches on as the baby continues to put its own birth on hold. Elsewhere, Quark sells Odo a container that holds a baby Changeling.
Captain Sisko lands on a planet near the Badlands to meet with someone who says that they have information on the former Starfleet officer Michael Eddington, now the leader of the Maquis. Unfortunately, Eddington is quite a few steps ahead of Sisko and his crew.
A Cardassian message is received from the Gamma Quadrant and Captain Sisko asks Garak to decipher it. Unfortunately, Garak informs the Captain that it's only a five-year-old survey mission. However, a while later Garak is caught by Doctor Bashir readying himself for a trip through the wormhole.
Stardate 50564.2: Worf and Garak, who travelled through the wormhole to find the source of Enabran Tain's message, are captured by the Jem'Hadar and brought to an internment camp. There, Garak is reunited with Tain before the old Obsidian Order leader dies. Meanwhile, Deep Space Nine monitors Starfleet listening beacons go down one by one. Fearing that a Dominion attack is imminent, Captain Sisko prepares to close the wormhole permanently. However, a saboteur destroys the pulse that would close the wormhole. Seconds after the pulse dies out, Dominion warships enter the Alpha Quadrant.
Rom attempts to tell Leeta about his feelings for her. As a very shy individual, he stumbles at every chance. At the same time, Leeta catches the eye of Lewis Zimmerman, a doctor who created a program to create a holographic image of a doctor to serve in certain Starfleet situations. The doctor has come to see Julian Bashir, because he has been selected to be the next installment of the holographic doctor.
Odo has a chance encounter with a woman in Quark's who later tries to break into the ship's computer system. While not sensing any real criminal intent on the woman's part, Odo does feel that the woman is in danger and offers his services as Deep Space Nine's Chief of Security. The more time that he spends with her, the more love he feels for her.
Chief O'Brien's son is at present going through a phase. Kirayoshi just can't seem to fall asleep and is crying all the time. Elsewhere, Quark, on the verge of losing his bar, becomes employed by his cousin, a weapons salesman. It isn't long before Quark's debts disappear... along with all of his Starfleet friends.
Former Cardassian Legate Tekeny Ghemor ("Second Skin") ventures to Deep Space Nine in order to help draw up plans against the Cardassian Empire and their new Dominion associates. Unfortunately, the Legate is dying and does not have much time left. At the same time, Gul Dukat calls Captain Sisko and requests that Ghemor be returned to Cardassia.
While Cardassian voles are being removed from Quark's, the owner laments his pitiful life. Being a Ferengi who is banned from doing business with other Ferengi is tough on Quark. Rom suggests that he pay a visit to mother while Leeta and he prepare for their wedding. All Rom has to do is make her sign the Ferengi Waiver of Property and Profit.
General Martok is called upon by the Klingon High Council to lead up a one-vessel search for a possibly lost Klingon ship near the Cardassian border. Taking Worf as his first officer and Dax as his science officer, Martok sets off on a ship whose crew has not seen victory in a long time.
Stardate 50814.2: After finishing up a long survey mission in the Gamma Quadrant, the tired crew of the Defiant heads back towards the wormhole. On their way, Jadzia Dax spots a planet with an unusual barrier around it. With the science officer confident that taking a look a the planet would not cause any problems, the Defiant passes through the planet's atmosphere. The barrier causes damage to the ship and they have to land to make repairs. As they look around for a place to set down, they are hailed by the inhabitants of the planet, who are the great-grandchildren of the Defiant's crew. The barrier created a temporal distortion, sending them back to the past by two centuries.
While Cadet Nog uses Captain Sisko's advice to make the Klingons aboard Deep Space Nine respect him, a captured communiqué from the Maquis brings grim news. As a last resort, the Maquis have used cloaking devices that they obtained from the Klingon Empire to mask thirty missles. The missles were then fired from a remote location in the Badlands towards Cardassia. The loss of so many lives could lead to even more deaths should the Dominion find reason to believe that humans had been behind the attack. A possible Quadrant war needs to be diverted and Sisko turns to the only man who can help: Michael Eddington.
Deep Space Nine's plasma manifolds are shot and the only viable source of new equipment for the former Cardassian station is from the previous owners. Since contacting the Cardassians is not an option, Captain Sisko sends his team to Empok Nor, Terok Nor's sister station that has recently been abandoned. The only problem is that the place could very well be booby-trapped.
Stardate 50929.4: The crew of Deep Space Nine has been growing increasingly wary of the Dominion-Cardassian threat. Jake senses that his dad is having trouble coping himself and sets upon obtaining an old baseball relic for Benjamin. Elsewhere, Kai Winn visits DS9 to meet with a Dominion liasion.
Stardate 50975.2: Rom and Leeta are set to be wed, but, aside from the wedding dress, they need one more thing: The Emissary to perform their ceremony. Captain Sisko agrees to do it. However, there may not be time as a fifth wave of Jem'Hadar ships enters the Alpha Quadrant bound for Cardassia. With the Dominion making their presence felt, the entire quadrant has become a hot zone.