Inai Boku wa Hotarumachi ni Iru

Despondent over the death of his best friend Takuya, Takeru wishes on a shooting star to meet his friend just one more time. A glimmer of light leads him to an ancient tree stump with a giant hole in it, a hole that impossibly leads to an entire city. It's the same city as his, the same people and places, but with two key differences: Takuya is still alive there, and Takeru isn't.
A 2-volume series.