The crew take shore leave on a friendly planet inhabited by people called Nechani. A group become interested in the Nechani's religious sites and take a tour. Kes is put into a coma when, out of curiosity, she touches a natural biogenic field. The Doctor cannot help, in part because the monks will not allow readings to be taken around the field. Neelix investigates and returns with a story of a King and his son. The son was seemingly injured as Kes was and the King went through an initiation in order to awaken him.
Janeway petitions the monks to allow her to perform the same ritual. The Doctor places a probe in her bloodstream, determined to find out the science behind the rituals. Janeway expects the course to consist of tests of physical endurance, mental discipline, and perhaps psychoactive drugs which would change her body chemistry, allowing her to pass through the field.
Janeway goes through the first series of tests; her guide warns that they are meaningless, the point is for Janeway to get in touch with the spirits. She ends up bitten by a creature which is supposed to allow her to contact the spirit world. Her guide seems to say that the spirits find Janeway's inquiries about Kes' plight inconsequential because she already knows how to fix Kes.
The Doctor thinks the venom from the creature might be the cure needed for Kes. It is not. Janeway convinces her command crew to let her go to the ritual site again, convinced that if she takes Kes through the field, it will work. Her guide allows it, indicating that Janeway's desire to go through is all that is needed. Kes is healed of her affliction. The Doctor comes up with a scientific explanation for how Kes was healed. Janeway seemingly expresses doubt that it was science.
Notes by Geo Cameron, author of the story, not the script: As someone with a background in shamanism, science and filmmaking I pitched the story to Star Trek. The script as it was written was different from the original pitch, but still good in my estimation. Tuvok and Chakotay swapped roles, and I'm not sure why. From an indigenous shamanic tradition, my original story put Chakotay on the side of alternate modes of perception. After all, people never stay in one 'normal' state of mind. We sleep, we dream, we wake, we feel cheery, grumpy, blissed out, tired, amused and so on. There is no one 'normal' state of consciousness or one 'normal' mode of perception. It is the only Star Trek to actually question scientific materialism, a fact I'm proud of. The idea that an interstellar future would quell spiritual experience is a bit odd. The capacity for such experience is hard wired into our brain structure, even a rationalist should be able to see that. My Dad was a Nasa scientist, and still always argued that "To say that the scientific method is the only method of human perception is, in and of itself, unscientific." This episode is not about blind faith, as some critics have said, but about the personal experience of the sacred, which is profound, personal and useful in daily life. People who believe in an afterlife tend to live longer physical lives--that's just one example. Anyway, science is one mode of perception, to make the best sense of the world we should be open to all modes.