Plot summary
The USS Defiant is sent on a mission to investigate a subspace anomaly. When Jadzia Dax, Miles O'Brien, and Julian Bashir take the runabout USS Rubicon into the anomaly, the entire runabout is shrunk to only several centimeters high, but the crew expects to return to normal once they exit.
While the runabout is in the anomaly, the Defiant is attacked by a Jem'Hadar ship, disabled, and boarded by Jem'Hadar soldiers. The Jem'Hadar commander, Kudak'Etan, proclaims the superiority of Jem'Hadar who were born in the Alpha Quadrant, and dismisses the advice of his more experienced, but Gamma Quadrant–born, second in command Ixtana'Rax. Since the Defiant' s engines are damaged, Kudak'Etan demands that Captain Benjamin Sisko repair the ship's warp drive. Sisko claims he needs his crew's assistance to do so, and Kudak'Etan grants his request over Ixtana'Rax's objections.
Meanwhile, the Rubicon and its crew escape the anomaly and return to the Defiant, still miniaturized. They enter the ship through a plasma vent and make their way into the engine room, where they discover the Jem'Hadar takeover. The Rubicon crew observe Sisko executing his plan: while Major Kira repairs the warp drive (working slowly to stall for time), Sisko, Worf, and Nog are attempting to regain control of the ship. O'Brien observes that Nog is attempting to override the ship's security codes, and suggests that they take the Rubicon to the bridge to assist them. When Kudak'Etan enters, Sisko complains about Ixtana'Rax's interference, driving an additional wedge between the two. As the Jem'Hadar departs, the Rubicon follows him through the door.
On the bridge, O'Brien and Bashir beam into a computer node to manually bypass the command codes. They manage to reroute the circuitry, granting Sisko control of the ship. Sisko is unable to take advantage of it, however: Ixtana'Rax, having discovered that the warp drive repairs are complete, orders the Defiant crew away from the computer consoles. Kudak'Etan orders that the ship return to a Dominion outpost immediately, ignoring Ixtana'Rax's concerns about sabotage.
The Rubicon returns to engineering and attacks the Jem'Hadar, and it and the full-size crew are able to overcome them. After the Defiant is retaken, the Rubicon re-enters the anomaly and is returned to its normal size.
Credits
Adapted from Wikipedia contributors, One Little Ship. Paragraphs and formatting adjusted; illustrations, reference markers, block quotations and non-story material omitted.