Board Thread:General Discussion/@comment-27907368-20160506131212/@comment-27620479-20160513153434

If we accept that Chara is the narrator, they stay with Frisk on the pacifist run, because there is narration after fighting Asriel. On neutral runs, or if Chara isn't the narrator, there is no clue what happens to them.

So, after a pacifist ending, either Flowey is left alone, probably with six human souls to play with, or Flowey and Chara, who isn't implied to have become a better person, are left behind, again, probably with the six human souls.

There goes your happy ending, better say goodbye.