Nostalgia. I played this game years ago... 2008, shortly after it was released, so I was in 8th grade at the time, and 14 just that past November. I'm 22 now. I loved the game then, still love it now. The little jackasses in the 3rd level that push you back upward. Always pissed me off, but never made me love the game any less. I found this game three times over after that, and got excited every time. Back then, I got the sexual element with the fertilization of the egg, the blastocyst, the fetus. I never thought/understood enough to interpret the meaning though.
It may seem odd, but I see psychosis, vivid hallucinations in this. Schizophrenia.
I see this taking place over the course of a shorter time period, maybe three or four months.
The trigger: rape.
The form her most prominent visual hallucination takes: her rapist.
Her rapist gets her pregnant. He's given her something, but has also taken a piece of her—left her feeling empty. She gets attached to her rapist though. Hence why her hallucination takes this form. His presence is frightening. She may know he's not real; however, she still finds comfort in him.
This hallucination has control over her, and has her do as her rapist has done; in being a part of her, she is "bringing them to him." Not rape others, but sleep with them, literally taking them in, the "significant pieces" of them. That could very well be their genes, as your genetics determine who you are physically, and to some extent, personality and intelligence wise.
She finally meets once person that she truly has a connection with, from whom she doesn't just want to take that significant piece and leave, and it eases the psychosis. It noted that the desire for his presence still lingered; he hadn't gone completely.
And then that person is gone, whether it be because she is left emotionally inept and disappeared (which it hints at), or he dies (also a possibility as it mentions her not answering her feelings when they called to her, possibly saying she waited too long).
When she "releases those pieces back into the world she never asked to be a part of," it could be alluding to aborting the child. Why I see a shorter time period. It would be the genetics of one man, but it would be symbolic of the others she'd slept with and taken pieces of.
As for a world she'd never asked to be a part of, schizophrenia requires a trigger AND a genetic predisposition. If a parent had the disorder, went unmedicated or refused treatment, she could have grown up in an abuse/unstable home. This could predispose her to growing attached to her rapist at all, and why her hallucination manifests as her rapist as she finds comfort in him.
And then "He" returns, and he's not happy, or she's afraid he's not because she had abandoned him. This would be her committing suicide. More slowly. She swallows a bottle of pills perhaps, noting the world fades to darkness. Her heart beats wildly in her chest. Could be a symptom of overdose. Everything fades to darkness. She had fantasized to being taken into nothing by him before. She may have suicidal for some time, or just at the onset of schizophrenia.
"From here on there is nothing, just as there was before."
The fade? Her heart stops beating, and she returns to "before".