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In "A Time to Stand" (S5E26) Starfleet mines the entrance to the wormhole, starting the Dominion War. No reinforcements are sent to defend Deep Space Nine so the fleet can destroy Dominion shipyards, and the Defiant is busy deploying the minefield. Once the minefield is activated, the Defiant and the Rotarran evacuate the remaining personnel on DS9 and leave under cloak to join the fleet.

However, what happened to runabouts that were stationed there? We don't see them leave, or attempt to defend the station (admittedly it's doubtful they could help defend against a fleet, but they were deployed alongside the Defiant for defence during "By Inferno's Light" (S5E15) so it's not unprecedented). We also know that the runabouts survive as we see them after the station is retaken (at least, we know that the seemingly indestructible Rio Grande survives - why anyone ever chooses to use a different runabout is beyond me!).

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    I don't remember this ever being stated, but given that runabouts are designed for long-haul missions, they probably sent them away as soon as the plan to lay the mines was devised, since they knew that they couldn't hold the station against the Dominion fleet. – Sava Oct 12 '18 at 22:49
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    They just... run about. – Paul D. Waite Oct 13 '18 at 20:30
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They appear to have left the station before the deployment of the cloaked minefield, or else they would have helped to lay it.

As to their location, it seems very likely that the runabouts were what Keiko, the 'kids' and the other Starfleet civilians (and their families) used to evacuate the station to Earth where they presumably remained until the station came back under Federation control.

SISKO: Try to look on the bright side, Chief. It won't be forever.

O'BRIEN: I know. And I understand why you ordered all the children off the station. Keiko and the kids will be a lot safer on Earth than here. But they've only been gone two days and I miss them already.

DS9: Call to Arms - Original Screenplay

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