While visiting the Nechani homeworld, Kes ventures into a shrine of the Nechisti Order and is struck by a mysterious energy burst, rendering her comatose. Unfortunately, when back on the ship, the Doctor can't help Kes because he doesn't understand her condition. The local magistrate tells Janeway that Kes violated a holy place that only monks may enter — and only after they have undergone a purification ritual to protect them from the energy field. Later, Neelix uncovers an ancient story of a king who went through the ritual to save his comatose son's life. Janeway requests permission to do the same.

The Nechisti Council approves Janeway's petition and the Doctor implants a subdermal bioprobe to monitor her physical condition during the ritual. A guide meets Janeway at the sanctuary and leads her to a room where three old people claim they are also waiting for the ritual to start, and have been there for as long as they can remember.

With Kes' life in the balance, Janeway impatiently demands that the ritual begin. The Guide hands the Captain a rock, and asks her what she sees. Janeway says she sees a stone, and is told to keep looking. The Guide takes her through a series of challenges, and hours later, an exhausted Janeway is told to put her hand in a basket, and an unseen creature called a "nesset" bites her. Janeway collapses, and the Guide puts her in an underground chamber.

On Voyager, the Doctor tracks the toxins from the bite as they course through Janeway's bloodstream, theorizing it might be the key to treating Kes. In a vision, Janeway asks the spirits to restore Kes' health, and her Guide cryptically tells the Captain that she already has what she needs to save Kes, and ends the ritual. Janeway returns to Voyager, where the Doctor prepares a cure from the toxins in Janeway's system. Yet when he applies it to Kes, she actually gets worse. Baffled, Janeway confronts the Guide, who sends her back to the waiting room.

The Council Members — the three old people Janeway encountered earlier — chide Janeway for having no faith in the spirits just because she can't scan them with her technology. Janeway realizes that if she's going to save Kes, she has to believe — if not in the spirits, then in her own faith that she can help Kes. Her only option is to take Kes back through the energy field, even though scans show it's deadly. Against Chakotay's and Neelix's advice, Janeway carries Kes into the shrine, and this time — whether it's due to the Captain's altered biochemistry or her newfound irrational faith — the energy field doesn't harm them, and Kes recovers.