[MU] Saya no Uta

Saya fixes Futomini's vision and once he discovers the bodies he suddenly gets his morals back and calls the police and he gets arrested for the murders and is declared insane and locked away for the rest of his life. Saya visits Fuminori once and, refusing to let Fuminori see her and hear her real voice, communicates using texts messages in a cell phone passed through an opening in the door. Fuminori confesses his love and promises to comfort her at any time. Saya leaves to search for her father, and Fuminori continues to wait in his cell. It is implied that the two never meet again.

Saya and Fuminori kill Kōji together. Afterwards, it turns out that Saya has reached the last stage and ultimate goal of her life: reproduction. Saya dies while releasing a spore-like matter into the atmosphere—a mutating agent aimed at humans, created by researching the human genome obtained during sex with Fuminori. The agent is spread across the globe by updrafts, slowly turning the entire human population into members of Saya's species. The end of the story is seen from Ryōko's perspective, and it is implied that Fuminori, although without Saya, will see beauty in the world once again since it will be filled with her kind. However, though this ending is described as beautiful in Fuminori's eyes, it is very dark to the rest as everyone else will now have to suffer in Fuminori's place.

Gotta say though, doesn't turn out well for everyone else though, that and tentacles were never my thing ;{

three possible endings: 1)Fuminori isolated after becoming 'normal' 2) Saya's reproduction 3) True Ending w/ only Koji left alive?

The lack of any morally 'happy ending' caught me off guard, although I was expecting that from its premise.

Yes there are only those 3, the 2nd on your list is considered the True/"Happy" end.