"Crossover" is the 23rd episode of the second season of Star Trek: Deep Space Nine.
"Medical log, supplemental. Major Kira and I are returning home after opening the hospital on New Bajor, the first Bajoran colony in the Gamma Quadrant."
As Major Kira and Doctor Bashir make their way back to Deep Space 9, Kira asks Bashir to take control of the runabout USS Rio Grande, as she has a headache and would like to meditate. As their runabout drops out of warp, the warp field does not collapse properly and they are engulfed in a white flash upon entering the Bajoran wormhole. When they exit the wormhole in the Alpha Quadrant, they are shocked to see the station is gone, instead it is orbiting Bajor much as it did during the occupation. Before either of them can react, the runabout's sensors detect a Klingon Vor'cha-class attack cruiser moving towards them. Two Klingon officers beam aboard the runabout and are shocked to see Kira. Apologizing profusely, they offer to escort her back to the station; she simply nods, obviously confused.
Upon arriving at Terok Nor, the two Klingons confer with a Cardassian officer named Garak. Bashir and Kira board the station, where they are confused to see Garak and even more confused to see another Kira Nerys...