Board Thread:General Discussion/@comment-27907368-20160412010659/@comment-27620479-20160508044517

The human souls are unaccounted for at the end of the game.

If you do pacifist, you may have missed this detail, because you don't want to admit that you have probably left Flowey behind with a source of determination that is known to override Frisk's.

On a neutral run, the souls rebel against Flowey. They are seen leaving Flowey's body, but then they just disappear. Even in the endings, where Undyne wants to kill the protagonist, she doesn't just absorb one or more souls and go after them.

And in the genocide run? Frisk's soul can be sold to Chara. So, it must have survived erasing the world or being attacked, whichever is your interpretation. In both cases, it is reasonable to assume, that the other souls may be there somewhere too.