The Bajorans are about to select a new Kai now that the popular and respected Kai Opaka is gone. She had hoped to see Vedek Bareil become the spiritual leader of Bajor after her, but he is running against a formidable opponent: Vedek Winn. Major Kira has recently started a romance with Bareil. She loathes Vedek Winn, both for her politics and her personality, and has a strong suspicion she is responsible for a recent assassination attempt on Bareil.
Meanwhile, Odo has arrested a Bajoran man called Kubus, who has been exiled for collaborating with the Cardassians during their occupation of Bajor. Vedek Winn relieves Odo of the criminal and offers Kubus sanctuary in exchange for information about the Kendra Valley Massacre that occurred on Bajor during the war. The massacre claimed the lives of 43 Bajoran militia members (including the son of Kai Opaka), and it is rumored that it was a Vedek who tipped off the Cardassians. Winn is eager to find evidence that this Vedek was Bareil. Winn gloats to Kira that she is about to ruin Bareil's chances for becoming Kai.
The crew analyzes some records and the evidence is there: Bareil was responsible. In disbelief, Kira confronts him. He admits to being the Vedek who provided the Cardassians with the location of the militia. He then explains that if he had not done this, the Cardassians would have destroyed village after village until they were certain they had wiped out the militia. Bareil gave them the information to save a thousand villagers, at the cost of the 43 militia.
Kira is crushed. Soon after, she hears that Bareil has withdrawn his nomination for Kai, clearing the way for Winn to take the post. With further investigation, Kira makes another confusing discovery: proof that Bareil was not the source of the information. He had covered up for someone else. When she asks him about it, he admits to her that it was the revered Kai Opaka who had been the "collaborator". She had sacrificed the militia, along with her son, to save the villagers. Bareil had covered for her because the Bajorans needed to believe in her during this painful time in their history.