Five years have passed after the events of
Doukyuusei Kaizou ~Namaiki Musume wa Jikkendai ni Shiteshimae!~ when the protagonist successfully ostracized a girl he disliked who kept picking fights with him by "transforming her into a futanari" with his new drug and effectively silencing her socially.
The two are now living together.
The reasons of why are simple: they realized they were mutually in love and the protagonist also feels a deep sense of guilt for what he did and he still hadn't been able to return Miki's body to normal.
As a futanari, her libido would run wild at the slightest provocation, making it impossible for her to live a normal life.
Then, one day, the protagonist's research takes a step forward and it marks the beginning of a "special training" to restore Miki's body to normal and help her reintegrate into society.
[Edited from
DLsite]