As the show opens, a Bajoran transport carrying Kai Winn (Louise Fletcher) and Vedek Bareil (Philip Anglim) suffers a mishap, and Bareil is left injured. He is brought on board Deep Space Nine, where he is treated by Dr. Bashir (Alexander Siddig). They soon, however, find that he is braindead. After Bashir tries to console Kira, who happens to be Bareil's lover, he begins an autopsy. Bashir soon learns that Bareil's nervous system is still active even though his brain can't process. He theorizes that the radiation Bareil was exposed to must be the cause and so he attempts to revive him by regenerating his brain. Bashir succeeds and revives him. Kai Winn is pleased and wants Bareil to assist her in the negotiations with the Cardassians that were begun by Bareil. Bashir soon discovers that the revival has caused Bareil's blood vessels to be restricted and is damaging his internal organs. He advises Bareil to go into stasis so that Bashir can find a solution, but Bareil refuses so that he can finish the negotiations and create peace for his people. Bashir then considers giving Bareil Vasokin, a drug that would increase the blood flow to his organs and return him to normal but would ultimately damage his internal organs.
The talks resume, but Bareil's condition continues to deteriorate, especially with Kai Winn continuing to probe him for advice when he should be recovering. Eventually, the Vasokin treatments begin to inflict brain damage, and Bareil falls unconscious again. Bashir suggests a radical procedure – replacing the damaged part of his brain with a positronic matrix.
The surgery is a success, except for the fact that Bareil is still severely brain-damaged and can live only for several months, just enough time to hopefully conclude his negotiations with the Cardassians. His lover, Major Kira (Nana Visitor), speaks with him, but he barely recognizes her. He is no longer the man she fell in love with.
Bareil is kept alive long enough to aid in completing the negotiations, and the treaty is formed between Bajor and Cardassia. As Bareil's condition worsens, Kira insists Bashir replace the remainder of his damaged brain with positronic matrices, but Bashir refuses on the grounds it will remove any 'spark of life' Bareil has left. The episode closes with Kira at Bareil's bedside, regaling a slowly dying Bareil with the tale of how she first fell in love with him.