(written from a Production point of view)
Utilizing the Unreal Tournament game engine, Star Trek: Deep Space Nine – The Fallen focuses on the quest to find the lost orbs of the Pah-wraiths capable of releasing the "fallen gods." The Cardassians, the Dominion, and the Bajorans are all eager to obtain the artifacts for their own purposes – and only the Federation stands in their way.
The intro sequence depicts a team of Cardassian scientists, led by Terrell, studying a red orb during the final days of the occupation. Desperate to achieve a breakthrough to prevent her project from being shut down, Terrell orders her team to attempt a risky experiment on the orb. The orb responds by attempting to create a wormhole, quickly breaking the force field containing it and killing one of the scientists as well as two guards, causing the latter to be fused into the wall behind them in the process. With the station seemingly about to be destroyed, Terrell flees the lab.
Mission 1 - Marauders / Crusaders Edit
Six years later, the USS Defiant responds to a distress signal from the Bajoran science vessel Keel'Tuul. While Sisko boards the Keel'Tuul, the Defiant finds itself under attack by the alien race responsible, later identified as the Grigari. Worf fends off boarding parties while repairing the Defiant, while Sisko successfully rescues all survivors on the Keel'Tuul before the ship explodes.
Meanwhile, Major Kira visits Obanak Keelen, a friend from the occupation. Obanak has lost faith in the Prophets since the occupation and has come to worship the Pah-wraiths as the true Prophets, now leading a monastery of Pah-wraith followers. As Kira wonders whether or not she should help Obanak get permission to excavate an old temple on the Bajoran moon Jeraddo, the monastery is attacked by a group of religious zealots called the Kaal'Taan. Finding herself in the crossfire, Kira fights her way to the monastery's communication array to contact her shuttle and take herself, Obanak, and any survivors to safety.
Mission 2 - Desecration Edit
Back on Deep Space 9, maintenance crews have discovered the bodies of the two guards fused into the hull. Sisko reveals that he has had nightmares about the Jeraddo ruins and leads an away team there. Sisko, Kira, and Worf beam into an old mining complex at different points and find their way to the temple, fighting off both hostile wildlife and attacking Kaal'Taan. Inside the temple, the team discovers an ancient mural depicting three orbs being used in some kind of ritual.
Mission 3 Edit
While the crew analyzes the mural, Deep Space 9 is visited by a delegation from the Carnellian Circle, a Cardassian medical organization, to investigate the deaths of the two guards. The crew also discovered the Cardassian lab on the other side of the bulkhead the guards were fused into. Sisko leads the Cardassian delegation, led by director Dejar, there. After entering the lab, Dejar reveals herself as Terrell, calling in Cardassian soldiers, who knock out Sisko and kill a security guard. As Terrell reclaims the Orb, she triggers the counter-insurgency program to lock the crew out of most systems. Sisko pursues Terrell, while Worf attempts to cut off her escape and Kira restarts the station's computer core to purge the counter-insurgency program. The Cardassians also attempt to destroy Deep Space 9 with a trilithium bomb, which the crew successfully defuses. Despite all efforts, Terrell escapes with the orb.
Mission 4 - Odyssey, Part I Edit
In an effort to even the odds, Sisko receives orders from Admiral Ross to recover another orb, found years ago by the Federation starship Ulysses. The ship was ambushed by a Cardassian warship before it could study the orb and crashed on SRIII, a planet that ended up deep in Cardassian space after the war. Sisko and Worf beam down to the planet to recover the Orb and place charges inside the Ulysses to scuttle it, respectively.
While Sisko and Worf carry out their missions, the Defiant finds itself under attack by the Jem'Hadar. Shortly afterwards, Kira discovers that one of the crewmembers was a Changeling who sabotaged the ship. Despite Kira's efforts, the ship is captured by the Dominion; with it, the crew and the recovered Orb are taken to a Dominion prison facility.
Mission 5 - Odyssey, Part II Edit
Various circumstances allow Sisko, Kira, and Worf to free themselves. After recovering their equipment, Sisko returns to the Defiant and retakes it. Worf fights his way through the facility and recovers the Orb in the process before meeting up with Kira in the facility's courtyard. Following their return to the station, the Orb is kept there for safekeeping.
Mission 6 - Hass'Terral Edit
Subspace distortions reveal that Terrell has set up a lab on Hass'Terral to study the orb and turn it into a weapon against the Dominion. Kira volunteers to be surgically altered in order to impersonate a Cardassian scientist and infiltrate the facility, while Worf places demolition charges and Sisko steals research data.
The team meets up in Terrell's lab shortly after another experiment that has left several people dead or injured. An exhausted Terrell concludes that the Orb must be destroyed and pleads with Sisko to let her do so, claiming that it is evil. Before either can do anything, Obanak beams into the lab, accompanied by several Grigari. He reveals that he found the third Orb years ago and declares his intention to unite all three Orbs to have them create second Celestial Temple for the Pah-wraiths to inhabit. Terrell attempts to shoot one of the Grigari and is critically injured as a result. After Obanak leaves with the Orb, Terrell reveals to the team how the Orbs can be destroyed before succumbing to her injuries.
Mission 7 Edit
The Defiant returns to Deep Space 9 to find it overrun with Grigari. Sisko, Kira, and Worf enter different sections of the station to repel the invaders. Meanwhile, Obanak performs a ritual in the lab to summon the Pah-wraiths. He is successful, but the Wraiths quickly kill his followers before possessing him. The team encounters the possessed Obanak in their various segments before meeting in the lab. There, the combined firepower of all three proves sufficient to force Obanak and the Pah-wraith through the rift created by the Orbs before it collapses, destroying the Orbs in the process. Obanak himself is either killed or ends up trapped with the Pah-wraiths.
The epilogue has each of the three characters talking about the events of the game. Sisko expresses concern that he hasn't seen the last of the Pah-wraiths, alluding to the events of the series finale. Kira wonders what would happen if, rather than corrupting a formerly good man like Obanak, the Pah-wraiths were to find someone truly evil to use as a vessel, again foreshadowing the series finale. Worf declares that the crew must be vigilant about the Pah-wraith threat and must never allow them to get as far as they did again.
- Nana Visitor was among the actors who reprised their roles by providing the voices of their characters. Visitor commented: "It's funny, when I get recognized, it's usually by people hearing my voice. My looks change, but my voice is really recognized as being behind Major Kira, even if they're not looking and just hear my voice. I am pleased that they bothered enough to get me in there, that`s a big thrill. It seemed to be very quick, and essential. The guys connected to the game where charming people, and it was fun and I got to see what it was about, and what it looked like, before I went into a studio and laid it down. The look of it is pretty stunning. It was always interesting. 'Now, okay you die falling off a cliff.' 'Now you die drowning'. It was challenging, more challenging that people realize, because you're dealing with the ultimate of experiences in life and death, and deep moments of crisis, in a couple of hours. And it's more than you can imagine, every way to die and every way to be in crisis." 
- In 2005, an update entitled Convergence was released. Eric Reuter commented: "Convergence takes place on SRIII, site of the wreckage of the USS Ulysses, a matter of months after the conclusion of The Fallen. The alleged purpose of the facility was to construct a weapon capable of being deployed for planetary defense. The source of power for this weapon system relates directly to the story of the Pah-wraiths, and to the ancient Orbs that they fashioned. The weapon promised to be of immense power, and it could ostensibly be deployed to protect any civilization from attack… the Cardassians have other plans, however." 
- Avery Brooks and Colm Meaney were the only Star Trek: Deep Space Nine stars to not voice their respective characters in The Fallen.  Ezri Dax (Nicole de Boer) does not appear, as the game is set in the series' sixth season. Cirroc Lofton did not voice Jake Sisko as the character does not appear. Notably, The Fallen marked the only time that Terry Farrell reprised her role as Jadzia Dax after the character's death in DS9: "Tears of the Prophets".
- Some story elements from the Millennium novels were incorporated into the game's story line, including the Grigari race.
- The Vorta Luaran previously appeared in DS9: "Tacking Into the Wind", which takes place approximately a year after the events of the game. In both the relevant episode and the game, she is played by Kitty Swink, the wife of Armin Shimerman.
- Rom, Leeta, Kai Winn, Admiral Ross, and Morn all make non-speaking cameo appearances on the Promenade between missions.
- Michael Bell (Obanak) previously played Groppler Zorn in TNG: "Encounter at Farpoint", Borum in DS9: "The Homecoming", and Drofo Awa in DS9: "The Maquis, Part II".
- Author William Sims Bainbridge looks at the depiction of religion in The Fallen in his book eGods: Faith versus Fantasy in Computer Gaming.
- Rene Auberjonois as Odo
- Michael Bell as Obanak / Wraith Obanak / Bajoran Man
- Kurt Bonzell as Bajoran prisoner
- Michael Dorn as Lieutenant Commander Worf
- Richard Doyle as Bajoran Fanatic / Bajoran male officer / Obsidian soldier / Rogon'Ogar
- Paul Eiding as male Vorta / Starfleet officer / Bajoran scientist / Zurris
- Terry Farrell as Lieutenant Commander Jadzia Dax
- Michael Gough as Chief Miles O'Brien / Male Obsidian Order / Bajoran monk
- David Graf as First Tugol'atan / Bajoran officer / Obsidian soldier
- Zachary Harris as Klingon warrior / Xono'Clan / Bajoran monk
- Nancy Linari as Terrell / Dejar / Obsidian Order female / Bajoran female
- Kevin Richardson as Captain Benjamin Sisko
- Andrew Robinson as Elim Garak
- Armin Shimerman as Quark
- Alexander Siddig as Doctor Julian Bashir
- Kitty Swink as Luaran / Kijana / Bajoran officer female
- Nana Visitor as Major Kira Nerys
- B.J. Ward as Obsidian Order female / Computer voice / Starfleet officer female / Bajoran nun
- Andre Ware as Bajoran officer / Tugol'atan / Obsidian soldier
- Written by: David Mack
- Set Costumer: Fran Murphy
- Story by: Judith and Garfield Reeves-Stevens
- Voice Recording Director: Kris Zimmerman
Bajoran; Cardassian; Cardassian Union; corophizine; Danube-class; Deep Space 9; Defiant-class; Defiant, USS; Dominion; formazine; hydrocortilene; Jem'Hadar; Klingon; latinum; Memory Alpha; Miranda-class; Pah-wraith; phaser rifle; Prophets; Ross, William; Terok Nor; tricorder; United Federation of Planets; Vorta