What I gathered while playing the game.
Two opposing I guess pharmaceutical company's doing genetic research, the one kept there scientists enslave by means of a drug that made them become unstable, and there body's died and disintegrated if they did not receive regular injection's.
One of the female scientist escaped from the for sure Evil lab, and was about to do the die, and disintegrate thing, she injected the boy with her blood, (which somehow contained the genetic imprint of her body, and the I guess the Evil pharmaceutical company's genetic manipulation formula.)
The next day the boy was a carbon copy of the female scientist that escaped and injected him. except for possibly being a much younger version of her. (also inside the blood was the supposed DNA blueprint for some other scientists from that company.)
The boy's Aunt who was I guess raising the two boy's, there parents having dies some how, was a scientist from the other pharmaceutical company, and somehow understood what was happening. and was trying to prefect the formula, and use it with her Clone research. (There by managing to clone the scientist somehow with her also having her complete memories latter in the story. Allowing her or She-He to also help with the cloning experimentation.)
Problem was the clone's in order to be stable or the only clones that were stable were like shemale, or females with penis's.
So they wanted the boy in the female form to have babies or one of them thought that was the best way, to prefect the clone's so they could return to a body like there original one.
( not sure if the babies were just clones them selves or how that worked, I know He as a she had a couple or they were aborted or Birthed or something, I'm just not sure on that, and maybe I have it all wrong
)
The boy, as a girl had a majorly high sex craving, or extremely strong Libido.
At one point the Aunt created a formula that transformed him back into a Male, but he had all the memories of what happened to him, and the things he had done or were done to him as a girl, and started to commit suicide because he was totally freaked out by all that had happened.
The Aunt drugged him and forced the change back to a female, to stop the suicide, until she could maybe figure a way to return him to normal, with out having him commit suicide. (Which did not seem like was ever going to happen.)
At least something like that is what I gathered playing the game.
Yeah it is a convoluted mess, but I found it rather interesting, and enjoyable myself.