When Celestia attempted to heal Twilight, she failed to undo the effects of the Orichalum. But, unbeknownst to her, her spell saved the fallen princess's consciousness by transferring it to a flower, which gained sentience and Twilight's colors. Twilight awoke to see herself in an unfamiliar body, looking at her own corpse. Instantly, she knew what happened, and she also knew that she could not reveal herself like that.

So, Twilight hid, now under the name of Flowey. She watched everything from the shadows, yet, despite every attempt, she was unable to feel empathy, able to feel friendship, only hatred. Flowey stayed near her old body so she wouldn't forget her legacy and who she was. That was, until the Traditionalists ruined her corpse and vandalized her coffin. Not bothering to warn those whom were once friends, Flowey tunneled somewhere else.

Slowly, she forgot who she was, with only bits and pieces left. But one thing was growing stronger. Flowey realized that she needed a soul inside her, she knew that she was not whole, and that a single soul would be enough. When three humans by the names of Megan, Danny, and Molly, along with six other ponies from another world, arrived at the scene, Flowey, an entity forged from the death of Twilight, finally decided to reveal herself.

Flowey: You really think that it is all friendship and magic? Ha! In this land, in this world, IT'S KILLED OR BE KILLED!