I have a hunch that it was all a plan of Mizuki.
The shed belongs to her family.
She's the one who drags Nana into the virtual world.
She's the only one who "hears" a voice.
The two kissing on the top of the tower they spot are maybe Mizuki's wish (it echoes the last pages of chapter 21)
When they wake up inside the VR and see their own body, Mizuki wakes up, but when she kisses the sleeping Nana, some part of Mizuki is still inside the VR and echoes her thoughts (I won't accept it).
In the final chapters, it's obvious she masters the commands of that VR.
So, it all points to a plan of Mizuki to keep Nana by her side "forever" as consciousnesses inside a virtual world, therefore avoiding the graduation, the fact that "lilies" are forbidden in her house, and leaving fairy land.
In the end, they leave their uniforms (symbolically their bodies) behind and get naked to enter the VR.
So, what happens to their bodies is the unknown here. The absence of the machine is odd too.
But who cares? Theirs souls will be forever together.