Keiko O'Brien, possessed by an evil Pah-wraith, plans to eliminate the Prophets. The Pah-wraith forces Miles O'Brien to use DS9's systems to fire chroniton radiation at the wormhole — destroying both it and the Prophets — or else he loses his wife and his daughter Molly.
While on Bajor doing botanical research in the Bajoran Fire Caves, Keiko O'Brien is possessed by a Pah-wraith with a plan to eliminate the Prophets. The Pah-wraith forces Miles O'Brien to modify DS9's systems in order to be able to fire chroniton radiation at the wormhole — destroying both it and the Prophets — or else he loses his wife and his daughter Molly.
Being under an impossible time limit, O'Brien tricks Rom into assisting him with the modifications. He explains to him that this is a top-secret upgrade, and that he is to tell no one about what he is doing and why. Dax spots the modifications, and thinking there is a saboteur loose alerts the Operations staff.
O'Brien is forced to point Odo in the direction of Rom to divert suspicion from himself. Rom is incarcerated but refuses to divulge anything about what he was doing and why. He explains that he will only speak to O'Brien alone. While they are talking, he asks Miles why he is trying to kill the Wormhole Aliens, and Miles is finally able to understand what is going on, and why.
Odo is still suspicious, however, and confronts Miles while he is performing the last modifications. Miles knocks him unconscious, finishes the modifications, and calls Keiko to tell her it is done, and to meet him at a Runabout. However, on the runabout, Miles tricks the Pah-wraith and unleashes the radiation on it, expelling it from Keiko's body and killing it.