Kono Sora ga Tsuieru Toki ni

Main character lives happily with his lover and friends around him. But one day the world comes to an end. Protagonist's brother is looking for a leader in this crumbling post-apocalypse world and he finds the leader in protagonist's lover Sena who undergoes transformation suitable to call her God's child... The two people keep on living happily. However, the fate is not smiling at them.

[From vndbreview]