If we are talking back before the reboot movies, and in the mid-00s, and this is a standalone DS9 with no sequals made. Then I would set the movie 7 years after the series finale. Bajor is a part of the Federation, Cardassia has been mostly rebuilt. DS9 itself has been refitted with quantum torpedoes, holoemitters and an ablative generator; transphasic torpedoes and slipstream drive are still under research at Starfleet. The Klingon Empire has only rebuilt 70% of their fleet.
The early scenes we see a Naomi Wildman – now living on the station - see Tuvok and Harry Kim off as their time on a station is over and they have been reassigned; Tuvok to the USS Titan under Captain Riker to join in the latest joint task force with the Romulans to deal with the growing Reman insurrection movement, while Harry Kim to the USS Aventine, under Captain Ezri Dax, for a five year mission to search for Iconian gateways.
Kira is discussing turning over command of the station to Nog after she turned in her Starfleet commission to be more involved with the Bajoran government and be on the Council of Ministers. Quark pesters Nog to loosen restrictions on the station once given command from Kira.
Bashir is bantering with the EMH I program that’s been installed for the past couple of years, and has been approached to be the model for the EMH Mark V; EMHs II through IV all had various unfixable glitches and the Mark I EMH is the most stable version. O’Brien has been brought to the station to see how the upgrades to DS9 are working with the Cardassian systems, over the objections of Keiko. Garak has replaced Ezri in Bashir’s life at this point, as Ezri chose to focus on her career instead of her relationship with Bashir.
DS9 detects a Borg cube come out of a transwarp hub, one of the few surviving Borg vessels that have been seen since Voyager’s return. There is a standoff between the cube and the station, that is then disrupted by the return of Sisko. The Borg attempts to assimilate Sisko, but he proves impervious, and in a demonstration of his new powers from the Prophets, manages to make the Borg Cube phase out of existence. After the reunion with the DS9 crew, he manages to settle with Kassidy and their child on Bajor.
Gul Macet and an aide are searching the fire caves, the last known whereabouts of his more famous cousin, Gul Dukat to figure out what happened to him, as Dukat has been listed as MIA by the Cardassian government. Using a copy of the Book of Kosst Amojan that was created by Vedek years before the Occupation, he releases the Pah Wraiths and becomes possessed by Pah Wraith spirit of Dukat. By channeling Dukat, Macet becomes a vengeful individual over being trapped in the fire caves, and tests his powers by vaporizing the aide.
Gul Macet leaves the caves and head to Cardassia where there are Jem’Hadar soldiers hiding out in remote areas, unaware that the Dominion War has been over for the past seven years. Macet manages to possess them and use them as an army to move in on the democratic capital. When news breaks that there is a Pah Wraith government that has taken over Cardassia with Gul Macet as the head of it. Cardassian troops attempt to retake it, but just fall under the control of Macet.
When Sisko learns of this, he is on Earth with his dad and Jake as he tries to both catch up with his family and to get some space from the Bajorans that hold mass outside his home on Bajor. Sisko is at a crossroads. Macet and the Pah Wraiths must be confronted, but knows from his time with the Prophets that doing so will both destroy Bajor and permanently take him away from Kassidy and their child, who he has been getting acquainted with. Because of his abilities, he can bring certain individuals back from the dead. He choses to bring back both Jadzia and Curzon Dax to ask for their advice; they tell him to confront Macet.
Meanwhile, the Pah Wraith-influenced Cardassian fleet manages to launch an attack on Bajor, and on several Starfleet vessels including the Aventine far from Bajoran space. This inspires Kira to go to the Gamma Quadrant to get help from Odo, hoping that he will have influence over the Jem’Hadar.
Upon return from the Gamma Quadrant, the Defiant has a battle with a Keldon class vessel in the Badlands, only to be ambushed by several Galor class warships. The Defiant receive assistance by a pair of ships led by Martok, returning from a conference with Grand Nagus Rom on Ferenginar. DS9 manages to fight off the Macet-led fleet, but Macet boards the station looking for a confrontation with Sisko, and the Jem’Hadar troops ransack Bajor as they also search for Sisko. Both the station and Bajor are evacuated as Sisko makes his way to DS9; the Ent-E takes him there as Sisko’s power’s have limits when it comes to travel, and Sisko has a moment with Picard, where they discuss the Borg, Worf and Q. After dropping Sisko off, the Ent-E goes to Bajor to assist with the evacuation.
There is a final epic battle that is Sisko vs Macet; Prophets vs Pah Wraith, that results in the destruction of the station. There is a scene where the Prophets explain to Sisko that the Prophets can finally retire now that the Pah Wraiths have been wiped from the galaxy. The Bajor of old that worshiped the Prophets has been destroyed, and a new Bajor that looks to the Emissary can take hold. And he can return to his old life; the Prophets withheld that bit from him to make sure he completed his task. Sisko then returns to Bajoran soil, powers removed and he is mortal once more.
Starfleet announces plans to build a new starbase, one inspired by the design of Deep Space Nine. Under Odo’s command, the remaining Jem’Hadar become a guard of sorts for the Bajoran government. Quark sees the destruction of DS9 as an opportunity to branch Quark’s out to a number of world in the Alpha and Beta Quadrants. Bashir and Garak set out to live on. The Defiant under Nog get reassigned to be closer to Earth. The Aventine is rebuilt and sent back out on her mission. And the final shot is focus on Morn doing something and about to speak.
