The USS Defiant is sent on a mission to investigate a subspace anomaly, which could yield significant technological advances for the Federation. Jadzia Dax, Miles O'Brien and Julian Bashir take the runabout USS Rubicon into the anomaly in order to take readings, tethered to the Defiant by a tractor beam. As a side-effect of entering the anomaly, the entire runabout is shrunk to only several centimeters high, but the crew expects to return to normal once they exit. However, during the procedure, the Defiant is fired upon by a Jem'Hadar attack ship, disabled, and boarded by Jem'Hadar soldiers. The tractor beam is disconnected, leaving the runabout in the anomaly where the Jem'Hadar cannot detect it. Aboard the Defiant, the Jem'Hadar discover that the engines are damaged. The Jem'Hadar First Kudak'Etan celebrates victory, declaring that the new generation of Jem'Hadar born in the Alpha Quadrant are superior to those in the Gamma Quadrant. He overrules his Gamma-born Second Ixtana'Rax, despite his status as an "honored elder" and greater experience. Kudak'Etan reports in to his Vorta superior, Gelnon, who orders him to prioritize repairs to the Defiantwarp drive and get underway to the nearest Dominion outpost, while the Jem'Hadar ship departs for another mission. Meanwhile, the Rubicon escapes the anomaly and sets course for the Defiant, unaware that they have not returned to their previous size, as their sensors are offline. Discovering their predicament and unable to communicate with the Defiant, the runabout decides to enter the ship through a plasma vent. Meanwhile, Kudak'Etan has Benjamin Sisko brought to the bridge and demands that he help the repair efforts on the warp drive. Sisko claims he needs his crew to do so, and Kudak'Etan grants his request over Ixtana'Rax's objections. On the way to the engine room, Ixtana'Rax threatens Sisko, and reveals the dissent between the Alpha and Gamma Jem'Hadar. Meanwhile, after narrowly avoiding being destroyed when the impulse engines are restarted, the Rubicon makes its way into the engine room and discovers the Jem'Hadar takeover. The Rubicon crew observe the Starfleet crew members in engineering, and realize their plan - Sisko has Kiraconduct repairs, though slowly to stall for time, while 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. Sisko realizes they need an alternate plan if they are unable to regain control of the ship, and instructs Worf to plant a virus which will destroy the ship when it enters warp. Meanwhile, the Rubicon sneaks onto the bridge, where O'Brien and Bashir beam into a computer node to manually bypass the command codes. Despite O'Brien's initial disorientation, they manage to reroute the circuitry. At the same time in engineering, Nog believes he has cracked the codes but Ixtana'Rax orders the Defiant crew away from the computer consoles, revealing he is aware of the crew's delays, and the warp drive has actually been operational for an hour. Kudak'Etan orders the Starfleet crew locked up, and that the ship make way to the outpost, ignoring Ixtana'Rax's concerns about sabotage. The Rubicon then attacks the Jem'Hadar, and together with Sisko and the crew are able to overcome them. Sisko floods the ship with gas to knock out the remaining Jem'Hadar and orders Kira to disable the virus before the ship is destroyed. After subduing the Jem'Hadar and taking back the ship, the Rubicon re-enters the anomaly and is returned to its normal size. Back at Deep Space Nine, however, Odo and Quark tease O'Brien and Bashir, wondering if they have returned slightly shorter than when they left, and share a laugh as the two rush to sick bay in a panic.
