Star Trek: Deep Space Nine

One Little Ship (6x14)

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Stardate: 51474.2 Dax, O'Brien and Bashir take the runabout U.S.S. Rubicon to explore a nebula, when they shrink to a size where the runabout is four inches long. The Defiant is taken over by the Jem'Hadar, and it up to the tiny crew of the Rubicon to get it back.