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Weeding out the references[]
In order to complete figure out which runabout was what, with 79+ appearances/references, there will be a degree of heavy weeding to figure out which appearances had named/unnamed Danube class runabouts, reused footage, and so forth, so as to avoid a number of "unnamed ships" that are in reality part of the station's regular complement.
- DS9 Season 1
- "Emissary"
- USS Rio Grande (ID per dialogue/script; Sisko/Dax to Denorios belt/Gamma Quadrant)
- USS Yangtzee Kiang (ID per dialogue; Kira/Bashir/Odo to Denorios belt)
- USS Ganges (inferred; one of three runabout class ships dropped by E-D)
- "Past Prologue"
- USS Ganges (ID per dialogue; Sisko/O'Brien to Bajoran moon/Gamma Quadrant)
- USS Yangtzee Kiang (ID per dialogue; Kira/Tahna to Bajoran moon/Gamma Quadrant)
- (Rio Grande referenced in script sets, but apparently/decidedly unused/unseen)
- "Babel"
- USS Yangtzee Kiang (extrapolated per reused "Emissary" footage; Kira/(Ren) to Bajor)
- "Q-Less"
- USS Ganges (ID per dialogue; @Landing Pad 5; docking hatch viewed only; Dax/Pauley/Vash from Gamma Quadrant)
- "The Passenger"
- USS Rio Grande (ID per dialogue/script; Kira/Bashir from ?)
- USS Rio Grande again (ID per dialogue/script; "Bashir" to hijack Norkova)
- "Vortex"
- USS Rio Grande (ID per dialogue/script; Sisko/Dax)
- USS Ganges (ID per dialogue; aka Rio Grande per script; Odo/Croden)
- "Battle Lines"
- USS Yangtzee Kiang (ID per dialogue; Sisko/Kira/Opaka/Bashir; destroyed)
- USS Rio Grande (ID per dialogue/script; Runabout Pad "C"; O'Brien/Dax)
- "The Storyteller"
- USS Rio Grande (extrapolated per recycled footage; Bashir/O'Brien)
- "Progress"
- USS Ganges (ID per dialogue; Dax/Kira)
- Ganges again (extrapolated per recycled footage earlier in the episode; Runabout Pad 3; (Kira)/2 Baj security officers)
- [?] (Bashir)
- [?] (Sisko: "There'll be a Runabout standing by.")
- "Dramatis Personae"
- USS Rio Grande (extrapolated per recycled footage from "Emissary"; Dax/O'Brien)
- "In the Hands of the Prophets"
- USS Rio Grande (archive footage)
- Airlock (maybe?) (Runabout Pad "C"; O'Brien)
- Inferred (Runabout Pad "B")
- Inferred (Runabout Pad "A")
- "Emissary"
- TNG: "Timescape"
- Enterprise-D runabout (Picard/Data/LaForge/Troi)
- DS9 Season 2
- "The Homecoming"
- USS Rio Grande (ID per dialogue/script; O'Brien/Kira/(Li) to Cardassia IV)
- Esso's transport 001 (docking hatch; Esso from Bajor)
- "The Circle"
- USS Rio Grande (extrapolated per reused "Emissary" footage; Runabout Pad "C"; Sisko/O'Brien/Li/Bashir to Bajor)
- "The Siege"
- USS Ganges (ID per dialogue; docking hatch viewed only; Jake/Starfleet families to Korat system)
- USS Rio Grande (ID per dialogue; docking hatch viewed only; Rom/Nog/dabo girl to Hanolan colony)
- USS Orinoco (ID per dialogue; unseen departing station)
- "Invasive Procedures"
- USS Orinoco (dialogue; @Runabout Pad "C"; interior only; Sisko awaiting Verad)
- "Cardassians"
- USS Rio Grande (extrapolated per reused "Emissary" footage; Bashir/Garak to Bajor)
- "Melora"
- USS Rio Grande (ID per dialogue/script; Sisko/Bashir/O'Brien pursuit of Orinoco)
- USS Orinoco (ID per dialogue/script; Dax/Melora/(Quark)/(Kot) to Gamma Quadrant)
- "The Alternate"
- USS Rio Grande (ID per deleted scene/script notes; Odo/Mora/Dax/Weld to Gamma Quadrant)
- "Armageddon Game"
- USS Ganges (ID per dialogue; O'Brien/Bashir to T'Lani III; destroyed)
- USS Rio Grande (ID per script; Sisko/Dax/(O'Brien)/(Bashir) to T'Lani III)
- "Whispers"
- USS Rio Grande (ID per dialogue; "O'Brien" to Parada system)
- USS Mekong (ID per dialogue; Sisko/Kira to Parada system)
- "Paradise"
- USS Rio Grande (ID per dialogue/script; Sisko/O'Brien to Orellius system)
- USS Orinoco (ID per dialogue; @Runabout Pad "C"; Dax/Kira pursuit of Rio Grande)
- "Shadowplay"
- USS Orinoco (ID per script; Dax/Odo to Yadara II)
- "Playing God"
- USS Mekong (ID per dialogue; damaged; Dax/Arjin to Gamma Quadrant)
- USS Rio Grande (ID per dialogue; Dax/Arjin to exterior of DS9)
- "The Maquis, Part I"
- USS Rio Grande (ID extrapolated per recycled footage; Sisko/Dukat to DMZ)
- "The Maquis, Part II"
- USS Rio Grande (ID per dialogue/script; Landing Pad "C"'; Odo/Bashir/Sisko to rescue Dukat)
- USS Mekong (ID per dialogue/script; O'Brien/Sisko/Kira/Dukat v. Xepolite ship)
- USS Rio Grande (ID per dialogue/script; Dukat/Sisko v. Maquis)
- USS Mekong (ID per dialogue/script; O'Brien/Bashir v. Maquis)
- USS Orinoco (ID per dialogue/script; Kira/Dax v. Maquis)
- "The Wire"
- USS Rio Grande (extrapolated per recycled footage "Emissary" footage; Bashir to Arawath Colony)
- "Crossover"
- (Rio Grande?; Kira/Bashir to Gamma Quadrant)
- "Tribunal"
- (Rio Grande)? (USS Orinoco per an early script draft; +recycled footage of USS Yangtzee Kiang; the O'Briens to vacation)
- "The Jem'Hadar"
- USS Rio Grande (ID per dialogue/script; Sisko/Jake/Quark/Nog/(O'Brien) to Gamma Quadrant)
- USS Mekong (per dialogue; Kira/(O'Brien)/Bashir v. Jem'Hadar)
- USS Orinoco (per dialogue; Dax/Odo v. Jem'Hadar)
- "The Homecoming"
- DS9 Season 3
- "The Search, Part II"
- USS Rio Grande (per dialogue only; simulated interior only; Sisko/O'Brien to destroy wormhole)
- "The Abandoned"
- Danube unnamed 001 (ship unseen; Odo/Jem'Hadar youth to Gamma Quadrant)
- "Civil Defense"
- Dialogue: "Get as many people as you can to the Defiant and the runabouts."
- Dialogue: "Jake, I want you to head for Runabout Pad "C"..." (ref Rio Grande/Orinoco?)
- "Heart of Stone"
- USS Mekong (per dialogue; reused footage from TNG (labeled Rio Grande) and DS9 (of Ganges from "Vortex"); Odo/Kira to Prophet's Landing/Badlands)
- "Visionary"
- USS Rio Grande (seen, but unidentified)
- USS Orinoco (seen, but unidentified)
- USS Mekong (seen, but unidentified)
- A fourth runabout (seen, but unidentified)
- "Improbable Cause"
- USS Rio Grande (per dialogue; Odo/Garak to follow Retaya)
- USS Rio Grande (reversed recycled footage of said ship from "Battle Lines"; Odo to cave planet)
- USS Mekong (per inference; Odo/Garak to find Tain)
- "The Die is Cast"
- USS Mekong (per inference; Odo/Garak piggybacked to the Gamma Quadrant; destroyed)
- "Family Business"
- USS Rubicon (unseen, per dialogue only)
- "Facets"
- simulated interior only (Nog)
- "The Search, Part II"
- VOY: "Ex Post Facto"
- Runabout unnamed 001 ("Starfleet runabouts")
- DS9 Season 4
- "The Visitor"
- Danube unnamed 003 (new footage)
- USS Rio Grande (recycled footage from "Emissary"; Jake to Earth)
- "Hippocratic Oath"
- USS Rubicon (per dialogue; O'Brien/Bashir to Gamma Quadrant)
- "Indiscretion"
- USS Rio Grande (ID per script notes; visible registry; Kira/Dukat to Badlands/Breen planet)
- "The Sword of Kahless"
- USS Rio Grande (per dialogue (was previously Mekong in script); Worf/Dax/Kor to Hur'q planet)
- "Our Man Bashir"
- USS Orinoco (ID per dialogue; "Landing Pad 3"; Sisko/Kira/Worf/Dax/O'Brien from a conference; destroyed)
- "Sons of Mogh"
- Danube unnamed 003 (recycled footage from The Visitor)
- USS Yukon (ID per dialogue; Kira/O'Brien into Bajoran space)
- "Accession"
- USS Rubicon (ID per dialogue, but unseen; Dax)
- USS Rio Grande (extrapolated per recycled footage from Emissary; Sisko, Emissary-2 to wormhole)
- "Hard Time"
- Rio Grande? (recycled footage; O'Brien/Kira from Gamma Quadrant)
- "The Quickening"
- USS Rio Grande (recycled footage from "Improbable Cause"; Kira/Dax/Bashir to Gamma Quadrant)
- Kira to Bashir: Whenever you're ready, contact the station and we'll have a runabout here within days.
- "Body Parts"
- USS Volga (ID per dialogue; Kira/Keiko/Bashir from...)
- "The Visitor"
- DS9 Season 5
- "Apocalypse Rising"
- USS Rio Grande (ID per dialogue/script; Sisko/Dax from Earth)
- "The Ship"
- Danube unnamed 004 (Sisko/Hoya/Bertram/etc. to Gamma Quadrant; destroyed)
- "Looking for par'Mach in All the Wrong Places"
- [unknown] (interior only; Kira/(O'Brien) to Bajor)
- "Nor the Battle to the Strong"
- Danube unnamed 007 (recycled footage of Rio Grande from "Improbable Cause"; Jake/Bashir to Adjilon Prime; destroyed)
- "The Assignment"
- USS Rio Grande (recycled footage; O'Briens to wormhole)
- "Let He Who Is Without Sin..."
- [?] (Worf/Dax/Bashir/Quark/Leeta to Risa)
- "Things Past"
- [?] ("Captain Sisko's runabout"; @Landing Pad 1; Sisko/Odo/Garak/Dax from ...)
- "The Ascent"
- USS Rio Grande (Quark/Odo to Federation Grand Jury)
- "Rapture"
- USS Rio Grande (recycled footage; Sisko/Kasidy to Bajor)
- "The Darkness and the Light"
- [?] (Kira to... )
- "In Purgatory's Shadow"
- [?] (Garak; ship he tried to take to Gamma Quadrant)
- [?] (Worf/Garak to Gamma Quadrant)
- "By Inferno's Light"
- USS Rubicon ("Garak's runabout"; Worf/Garak/Bashir/Martok/Romulan from Internment Camp 371; deduced as ) [ship again referenced in "Inquisition"]
- USS Yukon (per dialogue; @Runabout Pad "E"; "Bashir" toward Bajoran sun; destroyed)
- USS Rio Grande (named in dialogue)
- USS Volga (named in dialogue)
- "Doctor Bashir, I Presume"
- Danube unnamed 006 (new footage)
- "A Simple Investigation"
- Danube unnamed 006 (recycled from Dr. Bashir)
- "Blaze of Glory"
- [?] (Sisko/(Eddington) to prison starbase then Badlands; some footage later recycled to depict USS Gander)
- "Empok Nor"
- Danube unnamed 008 (O'Brien/Nog/Garak to Empok Nor; destroyed)
- "Apocalypse Rising"
- DS9 Season 6
- "Resurrection"
- Danube unnamed 009 (recycled from previous ep; docked at upper pylon but supposedly @Landing Pad "A")
- "One Little Ship"
- USS Rubicon (per dialogue; Dax/O'Brien/Bashir to...)
- "Change of Heart"
- USS Shenandoah (per dialogue; @Landing Pad "A"; Worf/Dax to...)
- "The Reckoning"
- Three evacuating DS9 (most likely Shenandoah, Rubicon, Rio Grande)
- "Valiant"
- USS Shenandoah (per dialogue; Nog/Jake from starbase to Ferenginar; destroyed)
- "Profit and Lace")
- Danube unnamed 003 (recycled footage from the Visitor)
- "Tears of the Prophets"
- USS Rio Grande (source?; the Siskos to Earth)
- "Resurrection"
- DS9 Season 7
- "Shadows and Symbols"
- USS Rio Grande (visually; Siskos/Ezri to Tyree)
- "Treachery, Faith and the Great River"
- USS Rio Grande (ID per dialogue, plus recycled "Battle Lines" footage; Odo/(Weyoun) from small barren moon)
- "Prodigal Daughter"
- Danube unnamed 006 (recycled from Dr. Bashir)
- USS Rio Grande (extrapolated per recycled footage from "Battle Lines"; Ezri to home)
- "Chimera"
- [?] (new CGI; visible (illegible) registry on fore and underside of aft, 73918?; O'Brien/Odo from ...)
- USS Rio Grande (recycled footage from "Improbable Cause"; Odo to Koralis III)
- "Penumbra"
- USS Gander (ID per dialogue; destroyed; Ezri/(Worf) to Badlands)
- "When It Rains..."
- NCC-73918 (inc. possible recycled Rio Grande footage; Kira/Odo/Garak to Cardassia)
- "Tacking Into the Wind"
- NCC-73918 (abandoned?; Kira/Garak/Damar to Cardassia)
- "What You Leave Behind"
- USS Rio Grande (extrapolated per recycled footage; Sisko to Bajor)
- [unknown] (docking hatch viewed only; Odo/Kira to Founders' homeworld)
- [unknown] (docking hatch viewed only; O'Brien to Earth)
- "Shadows and Symbols"