Starfleet Command decides to take the offensive in the war against the Dominion, and Sisko is chosen to lead the invasion of Cardassia. The first target is the Chin'toka System, picked for its diminished defenses. Unfortunately, the crew is unaware that the Cardassian/Dominion Alliance has secretly deployed hundreds of orbital weapon platforms to protect the system, and that Gul Dukat has returned claiming he has the key to destroying Sisko and the Federation.
Sisko and Klingon General Martok meet with Romulan Senator Letant and convince his people to join the invasion force. Later, the Bajoran Prophets — the mysterious aliens who reside in the wormhole — appear to Sisko in a vision and advise him not to go to Cardassia.
Sisko requests permission to heed the Prophets' warning, but Admiral Ross orders him to choose once and for all between his roles as the Bajoran Emissary and a Starfleet Captain. Sisko decides to proceed with leading the invasion, leaving Dax in charge of the station. Meanwhile, Dukat reveals his plan is to drive the godlike Prophets from the wormhole. Releasing an energy vortex from a Bajoran wooden figurine, his body is taken over by an evil Pah-wraith.
The invasion force reaches Cardassian space just before the defensive system becomes operational. Discovering all of the platforms are using the same power source, the crew tries to locate it. Back on the station, Dukat, possessed by the Pah-wraith, materializes in the Bajoran shrine and injures Dax critically, then destroys the sacred orb. The wormhole implodes and, at that instant, Sisko staggers back with the uneasy feeling that the Prophets are reaching out to him.
The power source is destroyed, disabling the weapon platforms and allowing Sisko's forces to invade Cardassian soil. However, their celebration is cut short by an urgent message from the station. They return, and although Dr. Bashir was able to save the Dax symbiont, Jadzia dies. Sisko, seeing that the wormhole has closed and all of the orbs have gone dark, fears that the Prophets have abandoned Bajor. Believing he has failed as both Emissary and Captain, Sisko decides he needs time to think about how to make things right. He takes a leave of absence from Deep Space Nine, returning with Jake to Earth.