Jake comes to his father for advice on where to take a Bajoran girl on a first date, his first ever. Unfortunately, Commander Sisko's time as head of Deep Space Nine is at a crossroads. Now, Major Kira brings him news that a Cardassian labor camp is still holding Bajorans on Cardassia IV. One of the prisoners is a man, thought to be dead, who could reunite Bajor. Kira requests a Runabout in order to rescue the Bajorans from their illegal imprisonment. Meanwhile, an ultra-nationalistic Bajoran group called The Circle makes their presence known on DS9.
Major Kira has been given some time off in order to prepare herself for her new post on Bajor. Li Nalas, the legendary Bajoran that Kira saved, has been given her post. With the tension mounting in the Bajoran capital, Quark provides Odo with new information that The Circle is being supplied weapons to counter the Bajoran military. Meanwhile, Sisko lets Kira know that he will do anything to have her reassigned to DS9.
The Circle, with Minister Jaro Esso leading their charge, makes a push for control of Bajor. Starfleet has ordered all Federation personnel to vacate Deep Space Nine, but Commander Sisko makes the choice to defend the station. All Federation personnel are evacuated save for all of the Starfleet officers onboard, who stand with Sisko. With the evidence that Cardassians are supplying The Circle with weapons, Major Kira and Lieutenant Dax find transportation down to Bajor to convince the Provisional Government of Jaro's misdeeds.
Stardate 47182.1: A plasma storm has engulfed Deep Space Nine. While a skeleton crew is kept on board to man the station, a freighter in need of assistance enters the sector. Once on board, however, the crew of the freighter hold the staff of DS9 hostage while the leader of the crew, a Trill, makes his demand.
Stardate 47177.2: While talking with Doctor Bashir at the Replimat, the Cardassian clothier Garak sees a Cardassian boy enter with a Bajoran man. Garak asks the man about the boy and is promptly bitten on the hand by the Cardassian. Further investigation reveals that the boy is one of the many orphans left on Bajor when the Cardassians left the planet. The matter becomes a political problem with Gul Dukat contacts Commander Sisko, and voices his hope to bring all Cardassian orphans home.
Stardate 47229.1: An Elaysian named Melora will be coming aboard Deep Space Nine in order to map more of the Gamma Quadrant. Since Elaysians can only function normally in gravity far less than other humanoid species, special modifications have been made to accomodate Melora. As she becomes used to life on the space station, another visitor has made it be known to Quark that the Ferengi is a dead man walking.
Grand Nagus Zek returns to Deep Space Nine, and he wants Quark to be in charge of the negotiation with a race from the Gamma Quadrant that will secure the Ferengi presence in a new corner of the galaxy. A very knowledgeable Ferengi named Pel, who has impressed Quark with his ability to recite the Ferengi Rules of Acquisition from memory, assists Quark in his endeavor.
Stardate 47282.5: Quark meets with a woman on Bajor who wants him to acquire a container. During the Cardassian's occupation of Deep Space Nine, the container was hidden in a wall located in one of the station's recently converted storage facilities. Quark believes that he is working for the woman's interests, but the woman has an accomplice and a history with DS9 that stretches back to Odo's first days as Constable in a case that involved Major Kira Nerys.
Stardate 47329.4: Commander Sisko's inabilty to sleep has caused him to realize that the fourth anniversary of the death of his wife had just passed the day before. Thinking about Jennifer, he meets a woman on Deep Space Nine who he becomes enchanted with. Meanwhile, a terraformer has docked at DS9 in order to have the warp engines on the science vessel Prometheus upgraded so that they will be ready for his mission to restore life to a dead star.
Stardate 47391.2: A ship from the Gamma Quadrant comes through the wormhole where the passengers are beamed aboard Deep Space Nine. The communicator at first has trouble dealing with the language of the new guests to the Alpha Quadrant, but it eventually manages to translate the language of the Skrreeans. Having been recently liberated from their overseers by a member of the Gamma Quadrant's Dominion, the Skrreeans have come through the wormhole looking for the planet Kentanna, where they will live peacefully.
A conman named Martus Mazur, trying to take a wealthy widow for all she's worth, is stopped by Odo who arrests him for attempting to swindle a couple on Deep Space Nine. While Martus sits in the holding area, his cellmate shows him a device which gives the user great fortune or great ruin. The old man tells Martus that the device has caused him nothing but heartache. However, a moment later the man is finally able to win one game before promptly dying. Martus takes the purple sphere from the dead man and begins to play the game.
Stardate 47391.7: Odo is paid a visit by the Bajoran scientist who studied him when Odo had first been found. The scientist, Dr. Mora Pol, has come to see Odo because of new information from the Gamma Quadrant: A planet has been found that could reveal the origins of the Changlings.
Stardate 47529.4: Doctor Bashir and Chief O'Brien board a ship above a planet whose populace had been wiped out by a genetic bioweapon, called Harvesters, to help to destroy the bioweapon used for a centuries long war. After many failures, the Kellerun and T'Lani, with the help of the DS9 crewman, are able to find the right radiation array that will destroy the weapon. Tragically, just as the last Harvesters are put in the radiation chamber to be destroyed, armed soldiers burst in and open fire. Bashir and O'Brien are able to fend off their attackers, but with more on the way their only option is to beam down to the planet's surface.
Stardate 47581.2: Chief O'Brien, aboard a Runabout, commences a personal log detailing the last 52 hours of an even that is linked to a Paradan peace conference aboard Deep Space Nine. Starting from the beginning, O'Brien records how all of those that he knows best aboard DS9 began to distance themselves from him in a very calculated manner.
Stardate 47573.1: While exploring the Gamma Quadrant for habitable planets to start colonies, Commander Sisko and Chief O'Brien transport down to a Class M planet only to find that they are unable to return to the Runabout that brought them to the new world. On the planet, they come across a group of human colonists who had crashed on the planet ten years ago, and had encountered interference on the planet that rendered useless the technology they had once used to survive.
Stardate 47603.3: While investigating an unusual particle field in the Gamma Quadrant, Lieutenant Dax and Odo come across rare omicron particles on a planet. Beaming down to the surface, they are swept up in a village's investigation to find out what happened to twenty-two of their fellow inhabitants. Back on Deep Space Nine, Kira, covering for Odo while he's away, welcomes Vedek Bareil to the station, and Commander Sisko assigns Chief O'Brien to work with his son so that Jake can prepare himself for the day he enters Starfleet Academy.
An initiate for the Trill host program has boarded Deep Space Nine to meet his trainer Jadzia Dax. A bit worried about Dax being his overseer, he is surprised to see that Jadzia Dax is nothing like he thought that she would be. In Ops, the crew try to purge the station of Cardassian voles before they become too much of a nuisance.
A Cardassian vessel suffering systems failure is docked at Deep Space Nine. While there, the three Cardassians onboard the ship are seen by Quark, who was once romantically involved with one of the Cardassians. Meanwhile, the Cardassian clothier Garak spots the three guests of DS9, which begins to worry the three. It isn't long before a Cardassian warship arrives.
A Klingon is put into Odo's jail for overextending his stay in one of the holosuites. He had been reenacting a famous Klingon battle fought decades before. Once Jadzia hears the Klingon's name, she lets him out of jail. The Klingon, along with his three companions, swore a blood oath with Curzon Dax eight decades ago to hug a Klingon known as The Albino, who killed all three Klingons' first-born sons. Now, The Albino has been found and the chance for vengeance is at hand.
A Cardassian vessel leaving Deep Space Nine explodes immediately after detaching from the station. Within hours, Starfleet admirals are breathing down Commander Sisko's neck for answers. Messages to Cardassia go unanswered and there is a fear that the Cardassian-Federation Treaty may be in jeopardy. A while later, Gul Dukat drops in unannounced in Sisko's quarters to discuss the incident.
Commander Sisko, Major Kira, and Doctor Bashir follow the warp signature of a vessel of the Maquis who had kidnapped Gul Dukat. Arriving at a Class M asteroid, the crew finds that Calvin Hudson has joined with the Maquis. The stakes have grown much higher and the Cardassian-Federation treaty has been brought to the brink of collapse. A single mistake now could lead to renewed hostilities between the two powers.
Garak, the Cardassian clothier on Deep Space Nine, begins to suffer from seizure-like conditions. Doctor Bashir tries to offer his services, but each time Garak refuses. Witnessing Garak attempting to purchase some merchandise from Quark sparks Bashir's curiosity and, with Odo's help, he is able to find out that Garak has an implant which is malfunctioning and could end up killing him.
Stardate 47879.2 Just before entering the wormhole from the Gamma Quadrant, the Runabout that Major Kira and Doctor Bashir were on suffered a plasma leak. They make it to the other side of the wormhole, but find themselves in a very different place.
With the choosing for the next Kai upon the Bajoran people, a former collaborator with the Cardassian Occupation returns from Cardassia in the hopes of returning to his home world. Instead, he is detained to await punishment for his crimes. Meanwhile, Vedek Bareil seeks the guidance of the prophets in order to bring himself to terms with the past.
Stardate 47944.2: Chief O'Brien embarks with his wife Keiko on their first vacation in five years. While on their way to their destination in a Runabout, they are stopped by a small Cardassian warship. Allowed to beam over, the Cardassians put O'Brien under arrest on charges of crimes against the Cardassian state. He is taken back to Cardassia Prime to await his inevitable execution.
Commander Sisko offers to take Jake on a science project through the wormhole to study a planet in the Gamma Quadrant. Jake brings Nog along to help him pass Mrs. O'Brien's science class. Along with Quark, who comes along to persuade Sisko to approve his new business scheme for Deep Space Nine, the Commander and the two boys begin their survey of a planet. On the first night, Commander Sisko and Quark are taken prisoner by the Jem'Hadar, the warriors of the Gamma Quadrant's Dominion.