Multiple realities
(covers information from several alternate timelines)

The following is a list of unnamed Danube-class runabouts.

By registry

By year

Transport to the Enterprise-D

A runabout assigned to the USS Enterprise-D...

...destroyed after being remotely piloted into power transfer beam

This runabout was utilized by four members of the USS Enterprise-D during their return trip from a three-day psychological conference on the effects of deep space assignments in 2369.

It was while on board this runabout and returning from the conference that Enterprise-D personnel Captain Picard, Counselor Troi, Geordi La Forge, and Data discovered the Enterprise-D and a D'deridex-class Warbird locked in a temporal fracture in the space-time continuum.

Ultimately, the runabout was deliberately destroyed via remote control by Picard from the Enterprise-D's bridge. The vessel was steered into a power transfer beam, which was the direct cause of the temporal fractures. (TNG: "Timescape")

The computer voice of the runabout was provided by Majel Barrett, who received no credit for this voice work.
The name and NCC registry were visible on the ship's hull as NCC-72452, the same as the USS Rio Grande from Star Trek: Deep Space Nine.

Esso's transport

Transport ship's airlock

This transport carried Minister Jaro Essa to DS9 following the return of Li Nalas. (DS9: "The Homecoming")

With exception of the airlock hatch connected to the station's docking port and corridor; This transport was only mentioned in dialogue.
It can be identified as a runabout by the airlock design patterns.

Maquis encounter at Teluridian IV

Around 2370, two Starfleet runabouts were encountered by the Val Jean near Teluridian IV. Although outnumbered, the Val Jean was able to escaped using the Maquis trick whereby they blew out the dorsal phase emitters and cut main power, making it look as if the ship was in serious trouble.

Commander Chakotay offered this trick to Captain Kathryn Janeway as an alternative to attack maneuver kappa 010, when the USS Voyager was under attack by two Numiri patrol vessels. (VOY: "Ex Post Facto")

These runabouts were only mentioned in dialogue.

Jem'Hadar youth transport

This runabout was taken by Odo into the Gamma Quadrant to reunite a Jem'Hadar youth with his people. (DS9: "The Abandoned")

This runabout was only mentioned in dialogue.
Odo simple stated that he would take a runabout, and was quite likely to be any the three known runabouts available at the time: USS Rio Grande, USS Orinoco, and USS Mekong.

DS9 evacuation

Four runabouts evacuating DS9 (one foreground, two left-side center, one right-side center)

Four runabouts, including the USS Orinoco, USS Rio Grande, USS Mekong and this runabout, departed from Deep Space 9 after it came under attack and was later destroyed by a Romulan warbird in a future alternate 2371. (DS9: "Visionary")

This was the first of two instances depicting the station ever having more then three runabouts on hand at any one time. In "By Inferno's Light", three runabouts, the USS Yukon, USS Volga, and Rio Grande were noted as still being at the station, while the USS Rubicon was away in the Gamma Quadrant.

DS9 runabout arriving

Runabout returning to DS9

This runabout returned to the station in 2372, around the time the Klingons were placing cloaked mines on the edge of Bajoran space. (DS9: "Sons of Mogh")

In alternate 2373, this runabout was returning to Deep Space 9 around the time the space station's civilian population began leaving en mass, following the recommending of voluntary resettlement. (DS9: "The Visitor")

According to the script notes, there was "Unusual activity evident, with transports and runabouts arriving and departing."

It once again returned to Deep Space 9 in 2374 during Grand Nagus Zek's visit. (DS9: "Profit and Lace")

DS9 runabout to Torga IV

This runabout was used by a team from Deep Space 9 to visit Torga IV in early 2373. The ship was later destroyed by a Dominion starship, with the loss of crewmembers Hoya, Bertram, and Rooney. (DS9: "The Ship")

DS9 runabout to Ajilon Prime

In orbit of Ajilon Prime

This runabout was used by Doctor Bashir and Jake Sisko in 2373 to attend a medical conference. En route back to Deep Space 9, the ship responded to a distress call from the Federation colony on Ajilon Prime which was under attack by Klingon forces. The runabout landed on the planet's surface but was later destroyed by Klingon aerial bombardments. (DS9: "Nor the Battle to the Strong")

DS9 runabout leaving

Danube runabout departing DS9.jpg

This runabout departed Deep Space 9 on three occasions in 2373. (DS9: "Doctor Bashir, I Presume", "A Simple Investigation", "Ties of Blood and Water") A fourth instance time was during the arrival of Kai Winn to the station aboard a Bajoran transport. (DS9: "In the Cards") It was later departing the station at the time of the arrival of a transport that was scheduled to deliver Miles O'Brien in 2375. (DS9: "Prodigal Daughter")

DS9 runabout to Empok Nor

This runabout was used by Chief Miles O'Brien's salvage team, consisting of Nog, Elim Garak, Pechetti, Boq'ta, Stolzoff, and Amaro, when they visited Empok Nor in 2373.

Some time after their arrival, this runabout was disengaged from its docking clamps and blown up by one of Cardassian soldiers left on the station, stranding the Starfleet crew there until help could arrive. (DS9: "Empok Nor")

DS9 runabout docked on upper pylon

Docked at Deep Space 9

This runabout was docked at one of Deep Space 9's upper pylons in early 2374.

When the mirror universe version of Bareil Antos came to the prime universe, he took Kira Nerys hostage and requested a "fast ship", with the apparent intention of taking it to "find a place where I can stop running" from the Alliance. Captain Benjamin Sisko requested that Odo clear a path to Landing Pad A, before informing Bareil that his runabout was waiting.

After climbing through fifty-seven levels to get to the landing pad, Kira stopped Bareil and disarmed him before he was arrested by two security guards. (DS9: "Resurrection")

This runabout was reused stock footage from "Empok Nor". It seems unusual that the runabout was shown docked to a pylon when it was indicated to be at the docking pads on the docking ring. However, it's position does explain why they climbed through so many levels from Ops, to get to where it was docked.
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