I really like how this story progresses.
It begins with an air of suspense. Does the flickering and fading of faith represent the waning of belief that the people of Gensokyo hold in the gods, does it represent the natural flow of faith with its wave like crescendos and low points, or could it be something more sinister? Sanae doesn't listen to her, possibly due to disbelief.
The flashback gives us a frame of reference, something to compare the Kanako of now to the Kanako of the past. Suwako warns her of protagonists, a warning Kanako should have heeded. It is possible that this is a story of a youth breaking away from a parent to seek her own path, for better or worse. Or, following the line that this could be something worse... perhaps Suwako was merely warning Kanako about herself... about how she may destroy her very identity to form a new one in the future.
When Sanae declares that Kanako must fight the protagonsists, she is stating that Kanako must fight her inner demons, she must reform herself. In doing so she not only changes her mental state, but first destroys the very symbol of her position... the mountain and the shrine which once stood on it. With physical barriers out of the way, Kanako faces her inner demons, the so called "protagonists" (named so because their presence helps kanako develop as a person). In the end, Suwako's warning becomes true, and Kanako successfully changes herself, becoming one of the protagonists.
