When Dominion sabotage is blamed for a planetwide power outage, Starfleet stations troops all over Earth to prepare for an invasion. However, Sisko is suspicious when he learns that the Red Squad, an elite group of Starfleet Academy cadets, was demobilized shortly after the State of Emergency was declared. By pretending to know about the mission, he tricks a Red Squad member into revealing that his group was ordered to create the power outage. Sisko fears Admiral Leyton is planning to overthrow the Federation government and replace it with military rule.
Federation President Jaresh-Inyo is unconvinced, but he agrees to force Leyton and his troops to stand down if Sisko brings him proof. Later, Leyton confronts him and tries to convince Sisko that martial law is the only way to deal with the Dominion threat. But Sisko refuses to participate in what amounts to treason against the Federation, so Leyton relieves him of his duties running Starfleet Security and orders him back to Deep Space Nine. On the grounds of Starfleet Headquarters that night, Sisko is approached by a Changeling in the form of O'Brien, who reveals that he is one of four Changelings on Earth. Their plan: use fear and paranoia to their advantage against the humans.
Sisko sends a message to Deep Space Nine and sets a plan in motion, then returns to his former office with Odo, who breaks into Leyton's classified Starfleet files. They surmise that Leyton's coup is scheduled to take place the day before the President's upcoming speech. Armed with new information, Sisko pays a visit to Jaresh-Inyo's office, where Leyton, Commander Benteen, and four security guards are waiting for him. They force Sisko to give them a blood sample in front of the President, and his blood promptly morphs into Changeling goo.
With Sisko in a holding cell, Leyton admits that he faked the blood test and tells Sisko he'll be set free after the coup. But after Leyton leaves, Odo helps Sisko escape and tells him the Defiant is headed for Earth. Sisko soon confronts Leyton with a phaser and demands his resignation — Lieutenant Arriaga, in custody on the Defiant, has admitted to helping Leyton make it look like a cloaked Dominion fleet was entering the Alpha Quadrant. Leyton responds that he has sent the Lakota to stop the Defiant, telling the Lakota crew that the Defiant is manned by Changelings.
The Lakota attacks the Defiant, and, realizing they have no choice, Worf orders his crew to fight back. In the heat of the battle, Leyton gives Benteen, who is commanding the Lakota, orders to destroy the Defiant — not just disable it. Uncomfortable with killing fellow officers, she instead shuts down her weapons and allows the Defiant to proceed to Earth. His most loyal officer having deserted him, Leyton realizes he has lost and removes his admiral's pips. With order restored on Earth, Sisko determines to not let fear conquer his homeworld for the Dominion.