@branch because "time and space was distorted". She basically popped out of nowhere into a reality where she's lived there for 13 full years with memories to match. She may have "realized" she was a goddess that very moment and since she was a baby at the same time, with no time to think "Jun!" and rush out the house to find him. Any time you mix alternate universes and/or time travel and/or into a story it gets all messed up.
@ToddSama come on, you know what everyone means. pedophile may not be the technical term for it at that age but it's very obviously the social term for it. Honestly if they're going to zap her into being from nothing as a pre-aged girl, it kinda makes me question why they made her 13 when he's 20, when she has always been his age throughout the story. I mean if they're zapping her into a full 13 years of life, might as well go for 16, or 18? But hey, woo, loli Nagi represent.
@bookwurm I mean, that's just the reality of life. People move on, see things in new lights. He cares for his childhood friend, but his obvious main choice was always going to be Nagi. If Nagi literally never returned, I could see him finding a fulfilling relationship with her. It's absolutely not weird at all.