When a serious accident nearly destroys a Bajoran transport arriving at the space station, Kai Winn manages to escape basically unharmed, but Vedek Bareil is critically injured. As Bashir operates on him while Kira worries, Winn informs Sisko that they were en route to a secret meeting to initiate peace talks with the Cardassian Central Command, and reveals that Bareil is the driving force behind the discussions. Unfortunately, Bashir is unable to save Bareil. However, as the doctor prepares to perform an autopsy, he notices a faint indication of life. After hours of intense work on Bareil's brain, Bashir is able to revive the dead man.
Bashir says Bareil could be back on his feet in a few weeks. But Winn is anxious to resume talks right away, and since Bareil is also determined, Bashir agrees to let him advise Winn from his bed. However, Bareil's circulatory system begins to fail, and Bashir tells him that he must be placed in stasis for an undetermined period of time. Feeling the obligation to bring about peace between Bajor and Cardassia, Bareil insists that Bashir find another solution. The doctor suggests an experimental drug that will let Bareil function for a few days — at the possible expense of his life. Against Bashir's judgment, Bareil tells him to try it.
Winn begins negotiations at the station, and it quickly becomes apparent that she is not comfortable in the role. Winn states to Sisko that, without Bareil, any hope of peace will die. Toward that end, she continues to ask him for advice, despite his obvious agony. Bashir then tells Bareil that the drug has already done irreversible damage to his organs. While artificial replacements can be inserted, Bashir recommends that Bareil go into stasis to avoid further damage, but he implores Bashir to do whatever is necessary to keep him going through the negotiations. The doctor turns to Winn, asking her to release Bareil from any more responsibility. But Winn is afraid to stand alone and refuses. However, when she returns to Bareil for another round of advice, his brain begins to fail.
The damage to the left side of Bareil's brain is irreversible, and Bashir grimly reports that he will not regain consciousness on his own. At the insistence of Kira and Winn, Bashir uses artificial brain implants to revive Bareil once again. Kira is by Bareil's side when he recovers from the surgery, and is devastated to discover that his feelings and emotions are basically gone. However, he retains the capacity to help Winn through the final negotiations, and the peace treaty is signed. But the other half of Bareil's brain soon begins to fail. Kira begs Bashir to save him with another artificial implant, but the doctor gently refuses, unwilling to reduce Bareil to a machine. Kira sadly accepts his words and asks to be left alone with the man she loves for the final hours of his life.