In order to investigate a rare subspace phenomenon, Dax, O'Brien and Bashir board the runabout, U.S.S. Rubicon, that is shrunken to four inches long. They are both assured this effect will be reversed once they leave the anomaly. Suddenly, the Defiant, tethered to the tiny runabout, is attacked and Sisko and the others are overtaken by the Jem'Hadar. The miniature runabout and its crew survives, but they exit the anomaly through a different route — without returning to normal size.
The runabout cannot enter the anomaly again without help, so Dax, O'Brien and Bashir pilot their vessel inside the U.S.S. Defiant. Meanwhile, the Jem'Hadar, unable to restore warp drive to the captured ship, force Sisko and his crew to guide them through the mechanical repairs. When the Jem'Hadar leader, First Kudak'Etan, sends away his Vorta's attack ship with assurance that the warp drive will soon be operational, Sisko seizes the opportunity to hatch a plan to retake the Defiant.
The runabout crew members find themselves in the Engine Room, where they realize the Jem'Hadar have overtaken the ship. Sisko, Worf, Kira and Nog work at the controls, trying to appear as if they are repairing the warp drive while they secretly retrace each other's steps. Dax sees that Sisko is trying to retake control of the ship from the operations console, but his plan cannot work unless Dax and her crew can pilot the runabout to the Bridge and help them from there.
They reach the Bridge, but are unable to release the command codes to transfer control to Sisko. O'Brien and Bashir leave the ship to do the job manually, with Dax beaming down oxygen molecules for them to breathe. Unaware of their crewmates' presence onboard, and feeling the time pressure bearing down, Kira continues to stall while Sisko infects the warp drive with a virus.
O'Brien and Bashir release the codes and are beamed back to the runabout. Just as Nog realizes that command functions have been transferred to Engineering, Kudak'Etan catches on to the crew's act. He prepares to put the ship in warp drive, not knowing about the computer virus. Just then, the runabout arrives, surprising the unsuspecting Jem'Hadar, and the "full-sized" crewmembers gain the upper hand. After disabling the virus, Sisko floods the ship with poison gas, subduing the remaining Jem'Hadar. The Defiant is liberated thanks to their tiny crewmates, who are soon returned to the anomaly and their normal size.