Board Thread:General Discussion/@comment-26006155-20160613103837/@comment-26006155-20160613213359

Doctor Alphys injected tons of golden flowers with determination, and the most they did was have clingier seeds and sprout in inhospitable places. Only Flowey achieved self-awareness, and since Alphys' goal of extracting souls from the Fallen Down monsters never panned out, any soul Flowey might have, had to have been with him originally.

My take on Chara is that she has the Player's soul. At the very beginning we put our own name in as the Fallen Human, believing that this is the Character we will be playing as, and the more our actions mirror what Chara would actually do, the more influence she has over us. On a genocide run Flowey says "You and your stolen soul" after you kill Toriel. Chara makes more and more independent decisions throughout the game, until finally taking over completely at the end of the Sans fight. Then to restore the world, you have to give Chara your soul, which by this time, is something she really has already.