Shelter tells the story of Rin, a 17-year-old girl who lives her life inside of a futuristic simulation completely by herself in infinite, beautiful loneliness. Each day, Rin awakens in virtual reality and uses a tablet which controls the simulation to create a new, different, beautiful world for herself. Until one day, everything changes, and Rin comes to learn the true origins behind her life inside a simulation.

Translation of the message at the end (I didn't translate its from r/anime):

To Rin
From : Dad
There was just so little time left after you were born.
I don't know how much love I managed to pour into raising you after your mother died...
But your smile kept me going. (^_^)
I would like to have come with you, but I couldn't.
I wanted you to forget everything and move on... I knew you'd be alright.
But you'll get lonely, and remember.
I know you'll grow strong, and read this letter some day.
I really wish we could have spent more time together. I'm sorry.
You were so young back then, too young to understand what they meant. So let me repeat...
My final words to you...