As the crew of Deep Space 9 try to prepare for a possible invasion by the Dominion, a fleet of Klingon ships, lead by the Klingon flagship decloak and take 'shore leave' on the station. While the Cardassians have sealed their borders, the Klingons have set up a plan to protect the Alpha Quadrant from the Dominion and are already stopping ships in Bajoran space to search them for Changelings. To get some answers about the Klingons, Sisko calls on the aid of the one person in Starfleet who knows most about the Klingons, Lieutenant Commander Worf. But Worf fears that the time has come again to choose between Starfleet and his own people.
Seizoen 4
After Worf learns that the Klingons plan to invade Cardassia on the suspicion that the new civilian government is replaced by the Founders. Sisko uses Garak to warn the Cardassians before the Klingon fleet reaches Cardassia, resulting in the end of the peace treaty between the Klingon Empire and the Federation. While Gul Dukat manages to save the Detepa Council as the Klingon fleet advances, the Defiant is needed to get them safely to DS9, and its aid will have far-reaching consequences for the Federation and the Klingon Empire.
It's several decades in the future. Jake Sisko is an old man, l4ing in his grandfather's house on the Louisiana bayou. On a rainy night, a visitor arr4es - a young woman who aspires to be a writer. Jake tells her the story of why he hasn't written in years. Long ago, he was on a trip with his father in the Defiant when an accident in the engine room caused his father to disappear before his eyes. Yet when Ben Sisko began appearing to him in the flesh, for a few minutes at a time, with years between appearances, it became clear that he was not dead, but trapped in subspace. Jake went on with his life, married, became a famous writer - but was forever haunted by his father's disappearance, and became obsessed with rescuing him. Now, Jake has finally found a solution...but what will it cost him?
Bashir and O'Brien, in the runabout Rubicon, are on their way home to the station after a routine biosurvey in the Gamma Quadrant when O'Brien detects a subspace magneton pulse which could indicate a ship in trouble. They track it to a planet thought to be uninhabited, where the runabout hits a plasma field and is forced to crash-land. The two are captured by a group of Jem'Hadar. But these Jem'Hadar are different - their leader, Goran'Agar, is actually free of their race's genetic addiction to the enzyme known as Ketracel-white, and has brought the others here in hopes of freeing them as well from the 'white' and the Dominion. Goran'Agar forces Bashir to work on a cure for the addiction, while O'Brien tries to convince the doctor to escape with him. Meanwhile, on the station, Worf finds he has a lot to learn about the way things are done in his new home, as he clashes with Odo over a smuggling investigation.
A smuggler friend of Kira's contacts her with news that some wreckage has been found which may be the remnants of a ship that was carrying Bajoran prisoners and a Cardassian crew - a ship that was lost during the occupation, and that was carrying another friend of Kira's. Kira is about to go and investigate when the trip is postponed slightly so that someone can join her: Gul Dukat. On the mission, Dukat reveals that he too has someone he is concerned about on the ship, a Bajoran woman with whom he had an affair. Kira learns also that Dukat's half-Bajoran daughter was also on the ship, and that Dukat's personal mission is to find her and kill her. Meanwhile, Kasidy Yates is not pleased by Sisko's reaction to her news that she may be taking a job that will let her stay on the station.
A Trill science team arrives on Deep Space 9 to conduct field tests on experimental techniques for creating artificial wormholes. The leader of the team is Dr. Lenara Kahn, a joined Trill whose symbiont was once borne by the wife of one of Dax's former hosts, Torias. Trill society has a strict taboo against 'reassociation' with past lovers, for which the penalty is exile - meaning that both symbionts will die with their current hosts. Therefore Dax and Lenara must be careful about interacting...but despite their best efforts they find themselves reawakening old emotional ties. What will Dax risk in order to be with her former love?
As Nog prepares to leave at last for Starfleet Academy, Quark receives a long-awaited payment from his cousin Gaila (the one with the moon): a shuttle of his very own. He offers to take Nog to Earth in it, with Rom piloting - but of course Quark has ulterior motives: smuggling illegal kemosite to Orion on the way back. However, due to the ship's having been sabotaged by Gaila, the three Ferengi (plus one stowaway) end up going through a time warp to Roswell, New Mexico in 1947. But far from trying to go home while leaving the timeline intact, Quark has other plans ...to stay and take over the Earth.
The Defiant is on a mission into the Gamma Quadrant to meet with a representative from the Karemma, who have been trading with the Federation, using the Ferengi as intermediaries, and who protest the exorbitant fees and taxes, which are actually the result of a misunderstanding perpetuated by Quark. But then two Jem'Hadar ships arrive to punish the Karemma for meeting with the Federation. When the Defiant goes after the Jem'Hadar, who pursue the Karemma ship into the atmosphere of a gas giant, it is attacked and heavily damaged. Bashir and Dax are sealed into a turbolift shaft, Kira cares for a gravely injured Sisko, Worf learns a thing or two about command, and Quark and the Karemma representative must defuse an unexploded torpedo that has struck the ship.
An elderly Klingon, Kor, who is an old friend of Dax, has returned to the station. Dax introduces him to Worf, whom Kor invites along on a quest: he has obtained a cloth found on a planet in the Gamma Quadrant - a cloth which was used to wrap the legendary Sword of Kahless. The Sword is a relic of Klingon history, stolen over 1000 years ago by the Hurk. Together, Kor, Dax, and Worf go to the planet where the cloth was found, and manage to find the Sword. But they have been followed there by Toral, the last member of the House of Duras, who once tried to seize power, and whose life was spared at the time by Worf. Kor, Dax, and Worf must journey through the caverns to escape, as ambition begins to turn Kor and Worf against each other.
Bashir is indulging in a holosuite program in which he is a glamorous British superspy on 1960's Earth, when he is joined by an uninvited guest - Garak. Meanwhile, the Runabout Orinoco is returning from a conference, with Sisko, Kira, Dax, Worf, and O'Brien aboard, when it explodes due to sabotage. The Ops transporter is damaged while beaming them off, but Odo and Eddington manage to store the patterns...in Bashir's holo- program, it turns out, where Bashir is startled to find the characters replaced by the images of the missing officers. While Eddington, Odo, and Rom figure out how to reintegrate their physical and neural patterns, Bashir must make sure the holosuite computer doesn't kill them off as part of his fantasy.
As Dax observes that the wormhole has been opening and closing for no apparent reason lately, news comes that an important Federation/Romulan conference on Earth has been bombed, and security cameras have recorded a Changeling in the room at the time. Sisko and Odo go to Earth, where Sisko is made the acting head of Starfleet security, as well as visiting his father with Jake. With the help of Sisko's old CO, Admiral Leyton, Sisko and Odo convince the Federation President to authorize stringent security measures. But it may be too late, as Earth's power relays are sabotaged and Sisko is forced to institute martial law.
A state of emergency has been declared on Earth, and armed Starfleet security officers are on the streets. But the activities of an elite cadre of Academy cadets on the night of the power outage arouse Sisko's suspicions. He and Odo investigate, and learn that the sabotage was caused not by Changelings but by 'Red Squad' under orders from Admiral Leyton, whose goal is to oust the President and take over Earth to fortify it against the Dominion. And Leyton is willing to do anything, even order one Starfleet ship to destroy another, to carry out his plans.
Bajor's new First Minister - Shakaar, Kira's old friend and the head of her former resistance cell - arrives on the station for negotiations with Federation delegates concerning speeding up Bajor's admission. No sooner is Shakaar aboard than there are threats on his life, and Odo must guard him around the clock, a task made especially difficult when Shakaar and Kira start getting close...very close. Odo, who is himself secretly in love with Kira, is caught up in emotional turmoil that starts to affect his ability to do his job, to the point of endangering Kira's and Shakaar's lives.
Kira leaves for a Cardassian outpost to attend a conference, escorted by Gul Dukat, who, after bringing his half-Bajoran daughter Ziyal home, has been reduced to commanding a freighter. When they arrive at the outpost, they find it destroyed by a Klingon Bird of Prey, which ignores Dukat's freighter. At Kira's suggestion, Dukat adapts a disruptor from the outpost and goes after the Klingons. When he succeeds in capturing the Bird of Prey, Dukat has the choice of returning to his old position - or striking out as a freedom fighter against the Klingons.
Worf's younger brother Kurn arrives on DS9, a broken, drunken outcast who has lost his seat on the Klingon High Council due to Worf's having sided against the Empire. Kurn demands that Worf perform the Mauk-to'Vor, a ritual in which by killing Kurn Worf can restore Kurn's lost honor. Meanwhile, Kira and O'Brien investigate mysterious explosions and Klingon activity near Bajoran space.
After Rom nearly dies from an ear infection due to Quark's refusal to give him time off to seek medical attention, and when Quark announces a pay cut for his employees to make up for losses incurred during the Bajoran Time of Cleansing, Rom decides he has had enough of his brother's heavy-handed management. He forms a union of all the bar and casino workers, to demand increased pay, shorter hours, and paid sick leave. When Quark laughs in their faces, the union promptly goes on strike. Meanwhile, Worf continues to have trouble adjusting to station life.
A battered old-style Bajoran lightship emerges from the wormhole with one passenger: Akorem Laan, a famous poet who left Bajor 200 years ago. Since he was the first person to meet the Prophets, and since they healed him, Akorem believes himself to be the Emissary, a role that Sisko is all too happy to relinquish to him. Akorem begins trying to lead Bajor back to the old days, when their caste system, the d'jarras, determined the careers people followed. Confusion results, and Sisko can only conclude that his mission to bring Bajor into the Federation has failed. Meanwhile, O'Brien tries to readjust his life when Keiko returns, pregnant with their second child.
While commanding the Defiant on a mission to escort a relief convoy to a plague-stricken Cardassian colony, Worf apparently destroyed a Klingon civilian transport which decloaked in the middle of a battle with two other Klingon ships. Now an extradition hearing is taking place on DS9, with Sisko defending Worf and Advocate Ch'Pok arguing the Klingon Empire's case. The tale of the mission unwinds in flashbacks, as Odo searches for the truth.
A shaken O'Brien returns to Deep Space Nine after his mind has been altered to make him believe that he spent the last two decades in prison. Accused of espionage by the Argrathi, he was g4en the painful memories of a twenty-year incarceration and released before his fellow officers could arrive to stop the punishment. While O'Brien is told what he went through was not real, the memories are too vivid for him to dismiss. When they begin to spill over into reality, O'Brien's false memories threaten his marriage and life on the station.
Jake can hardly believe his eyes when his father introduces him to a woman who appears and acts exactly like his late mother, Jennifer. Sisko reveals that this is Jennifer - at least her double from a mirror universe which Sisko once visited, where she was married to his now dead counterpart. Sisko leaves the two of them alone for awhile. When he returns, Jennifer and Jake are nowhere to be found. All that remains is a small device. Sisko uses it to transport to the mirror universe, appearing on the alternate Deep Space Nine. He is then taken prisoner and told that the rebels of this universe need his help in their fight against the tyrannical Alliance forces, led by Worf.
Jake meets a mysterious woman named Onaya, who claims to have 'a weakness for artists', and who says that she can help Jake to develop his talent for writing. His life is endangered as he falls deeper and deeper under her spell. Meanwhile, Lwaxana returns, pregnant and on the run from her husband Jeyal, who seeks to take their unborn son from her to raise by himself according to his people's customs. And Odo has a drastic solution to her problem.
Sisko is shocked and skeptical to learn that there is evidence suggesting that his lover, freighter captain Kasidy Yates, is smuggling supplies to the Maquis. However, the cloaked Defiant follows her ship, the Xhosa, on a run to the Badlands, where the crew witnesses Kasidy making a delivery to a Maquis ship...and soon Kasidy isn't the only traitor Sisko has to worry about. Meanwhile, Garak and Ziyal come to an understanding.
The Defiant returns from a mission to find that DS9 has been attacked by the Jem'Hadar. In pursuit of the raiders, they find another, damaged Jem'Hadar ship and beam aboard its crew and their Vorta supervisor, Weyoun, who tells Sisko that renegade Jem'Hadar have seized control of an Iconian gateway in the Gamma Quadrant. Sisko enters into an uneasy alliance on a mission to destroy the gateway before the renegades manage to restore it and gain the ability to instantly travel to any planet.
Bashir, Dax, and Kira are on a routine biosurvey mission in the Gamma Quadrant when they receive a 200-year-old distress signal. They follow it to a planet where the population, once a spacegoing culture, is suffering from an incurable fatal disease inflicted on them by the Jem'Hadar for defying the Dominion. Bashir becomes obsessed with finding a cure for the Blight, despite the opposition from natives who feel he is giving them nothing but false hope.
Quark returns from two weeks on Ferenginar and announces that he has been diagnosed with Dorek syndrome - a rare, incurable, fatal disease - and has six days to live. In order to pay off his debts, he offers his vacuum-desicated remains for sale on the Ferengi Futures Exchange, and is shocked when a 500-bar bid comes through. Naturally, Quark accepts - only to learn that he doesn't have the disease after all. But then his mysterious buyer - Brunt of the FCA - arrives...and he doesn't want a refund. Meanwhile, an accident forces Bashir to transfer Keiko's baby to Kira, and the parties involved must adjust to the unexpected situation.
As Gowron agitates for the Federation to pull out of a sector claimed by the Klingon Empire, Odo begins suffering from a destabilization of his molecular structure which makes it difficult for him to maintain solid form. The only answer is for the Defiant to take Odo into Dominion space and ask for the Founders' assistance. The Founders agree - in fact, they admit to causing Odo's condition to force him to return and be judged for killing another Changeling. Odo accepts their judgment, pays the price...and learns a secret that will shake the Alpha Quadrant.