Obsessed with capturing the traitor, Sisko pursues him in the Defiant. But when Sisko gives the order to fire, the Defiant experiences a massive computer failure — caused by Eddington. He leaves Sisko angry and humiliated, and facing a long trip home.
The Defiant is towed back to Deep Space Nine, and O'Brien begins the massive job of bringing the ship back on-line. Adding insult to injury, Sisko learns that Captain Sanders of the Starship Malinche has been assigned to apprehend Eddington since Starfleet feels Sisko hasn't himself been able to do the job in the past eight months. But when he learns that Eddington attacked Cardassian colonies in the DMZ with a biogenic weapon, Sisko sees his chance. Despite the fact that the Defiant is not ready, he prepares to take his ship back into space.
The ship lurches out of the station and soon encounters Eddington again, who taunts Sisko. The captain realizes too late that he was baited to false coordinates. As the crew sets off to find Eddington's real location, a distress call is received from the Malinche — Maquis forces ambushed and disabled the starship.
Sisko determines Eddington's next planetary target, but is too late to stop him from releasing his biogenic weapon into the atmosphere. The Defiant chases after Eddington's fleeing ship, but he cripples a transport vessel evacuating Cardassian civilians, forcing Sisko to break off his pursuit and rescue the helpless Cardassians.
Stumped as to how he's going to get Eddington, Sisko realizes that the renegade sees himself as a noble hero and Sisko as a villain. In order to stop Eddington, Sisko decides he must do something truly villainous. He prepares to poison the atmosphere of the Maquis colony in retaliation and reveals his sinister plan to all. Eddington is prepared to call his bluff. Sisko orders the deadly torpedoes launched, and the Maquis scramble to evacuate. Sisko says that he is prepared to eliminate every Maquis colony in the DMZ, and Eddington, realizing Sisko is serious, does the "heroic" gesture of offering himself in exchange. Eddington is captured, and Sisko's vendetta is finally over.