Board Thread:General Discussion/@comment-5413572-20160521063300/@comment-27524978-20160527122042

Since you've already done both the Pacifist and Genocide, Chara appearing is just a reminder that you've already seen what's there to see and that it's time to move on to another game.

Or Chara's being stupid to try to bring all the monsters to the surface with the humans and then kill everybody. Because when they possessed Frisk not only would they be at LV 1, but I doubt their murder spree on the surface would last long, due to all the superior weapons that the humans have. Chara probably later got shot or something, and Flowey's oblivious to what's happening up there as he is still in the Underground.