A Japanese game whose protagonist is a high-school student who lost his mother at a young age? Crikey, how original.
Either way, Cryostasis is the correct answer.
There is much more than that to the story.
But if I tell you why it would ruin a lot of major piece of the plot so I will refrain from doing so.
I have played Cryostasis and while it has great atmosphere it's plot is no where near the quality of YU-NO and that is understandable given the type of game Cryostasis is.
The brilliance of Cryostasis is not only in its plot, but in the way in which it is integrated into the gameplay. That's what it is about: being able to capitalise in full on the strengths of the medium. It's not difficult to tell a great story in a video game when you bereave it of most of the elements that make it a video game in the first place.