Magia Record Story A Voice From Beyond That Strokes the Ears
The following is a summary posted on 4chan's /pmmm/ general by Summary Anon.
The whole thing is a dream which Kanae shows Yachiyo to tell her that they are not victims of her imagined magic effect, but are deciders of their own destiny to sacrifice themselves to defend Yachiyo. The doppel event where Yachiyo decides to deal with their belongings is due to Kanae using both her and Meru's thoughts to affect Yachiyo.
The truth is that there is an afterlife for Puella Magis whose soul gems are crushed. They are able to turn into spirits and live in the afterworld. They can create things from imagination and can taste, feel and see them like it's real. They are also able to share the thing with others if they want to. The con is that they cannot affect the world of the living, though some gifted ones can hear them, and they can nudge people in the direction they want if they try hard enough, and can move objects, though it just causes a little rustle.
Meru turned into a witch, so there is no soul left for her to turn into a spirit, but her thoughts and feelings are retained by Kanae who has been watching over Yachiyo ever since her death. All the emotions and reactions of Meru are real, as are her regrets and thoughts, its just that she never gets to become a spirit.
In a way, Madokami guides the souls of Puella Magis turned into witches while Puella Magis whose soul gem got crushed get to live in the afterlife and visit the living whenever they want at the expanse of all forms of contact with the living.