My understanding is that this story is about continuation of some sort of bond between Eren and Levi. Eren loves Levi even through his after life and had been searching for him. (1st universe) He had found him but does not remember anything about his life before this one. Somehow Levi left (because he grew tired?) and Eren refused to believe it which explain the constantly throwing out of the food part. (2nd universe) Then he found Levi from another universe as it mentioned in the beginning about parallel universe. Desperate Eren doesn't want Levi to leave him again. So they had sex and Levi told Eren that he killed him then kills himself because he wants to be set free from Eren.
I want a spin-of for Miyoshi and that other guy. They are cute together.