Deep Space 9 prepares for a Dominion invasion. The crew trains for encountering changelings by hunting for Security Chief Odo throughout the station. Later Captain Sisko is hailed by General Martok. Martok asks for shore leave with his men, which Sisko grants. An entire armada of Klingon ships de-cloak.
Martok wants his ships to stay at DS9 to help counter a Dominion attack. As the Klingon soldiers spread throughout the station, they cause disruptions, and beat up Garak. Later a Klingon ship stops Kasidy Yates' freighter. Fed up with these issues, Sisko contacts Starfleet who sends Lieutenant Commander Worf to the station to help. Once on the station, Worf learns that the Klingon Empire plans on attacking Cardassia. Worf informs Sisko, who holds a meeting with Martok. Martok claims they need to attack Cardassia because it has been taken over by the Dominion. His proof is that Cardassian Central Command has been overthrown. Martok tells Sisko he will consult with Chancellor Gowron, instead he instructs the Klingon ships to begin their invasion of Cardassia.
Sisko is unable to warn Cardassia of the invasion because of the Federation-Klingon alliance. Instead Sisko lets "slip" to Garak the news of the invasion, who in turn warns Cardassia of the invasion. Once the Federation condemns the invasion, the Klingon Empire withdraws from the Khitomer Accords, ending the alliance with the Federation. Sisko contacts the new Cardassian government, and speaks with Dukat. Sisko convinces Dukat that he and the Council to evacuate Cardassia and meet with the Defiant to seek refuge at DS9. At the rendezvous point, the Klingon ships attack and the Cardassians are forced to join the Defiant. The Klingon ships follow the Defiant' back to DS9. Gowron urges Sisko to surrender, however unknown to Gowron, DS9 has been equipped with more than 5,000 photon torpedoes. The Klingon fleet attacks DS9, and is countered by several rounds of torpedoes. Many Klingon ships are destroyed, and Gowron orders his ships to target the shield generators. Klingon boarding parties beam into DS9, and after a hand-to-hand battle, the crew regains control of the situation.
Chief O'Brien is able to restore the shields to the station, and Starfleet reinforcements are on their way. This leaves the Klingon ships no choice but to retreat. Gowron warns Sisko that he has sided against them in battle, and he will not forget. Worf decides to stay aboard DS9, and he joins the crew as a Strategic Operations Officer, a command role.