Sisko faces a conflict between his Starfleet duties and his role as the Bajoran Emissary when an ancient Bajoran prophecy predicts a joint Federation-Cardassian project will lead to the destruction of the wormhole.
Now rejoined with his former mentor, Garak is ordered to interrogate Odo about the secrets of his people, while the joined Romulan/Cardassian attack fleet moves towards the Founders' home world on a mission of destruction.
Sisko rebuilds an ancient Bajoran space vessel from the blueprints, and he and Jake take the ship on a trip, attempting to prove that the ancient Bajorans went beyond their solar system without warp drive.
The Defiant is off to show the Federation's presence to the new Tzenkethi government. While underway the ship malfunctions and repeated instances leads Sisko to believe a changeling's onboard, engaging in sabotage.