Okay, here is my interpretation of the story.

Risa = Marisa Kirisame (Both PC-98 and Windows)
Risa's mother = Marisa's Mother
Hakurei shrine maiden (The one that disappeared) = Previous Hakurei shrine maiden
New Hakurei shrine maiden (Risa's friend) = Reimu Hakurei (Both PC-98 and Windows)

The story begins with Marisa's mum thinking about her regrets. She used to be a great magician tutored by Mima, who didn't fear the youkai. However, it lead to her destruction when she broke the taboo of human transmutation. Now she lives as a regular human in the human village, in constant fear of the youkai (such as Yukari Yakumo). When the shrine maiden disappears, she realises that she'll soon die to a youkai too.

Marisa's mum taught her daughter to stay near to shrine maiden, to be safe from the youkai she now fears.

Marisa, however, was inspired by Reimu's (the younger shrine maiden) power, and her Mother's fear of youkai. Thus, becoming a magician, tutored by Mima.

This story is basically about Marisa repeating the same mistakes as her mother. Just like her mother, Marisa now seeks power and doesn't fear the youkai, but eventually, just like it did to her mother, her power will be her downfall.
Marisa Kirisame is repeating the mistakes and the life of her mother, or in other words.
A Kirisame Reincarnation.