Flowey escaped the Capitol after wreaking havoc and killing many, and disappeared into the tunnels of the Underground; he is a master at hiding, even with his enormous, grotesque body, and will not be seen if he doesn't desire to be. The only way to know that he is near is the nigh-impenetrable darkness and a sense of dread that hangs in the air around him. He is the master of time and space in the Underground, possessing of far more determination than any other being, and hunts and consumes any monster unlucky enough to cross paths with him.
The Hunger was not kind to him, his form nor his mind. He has become a twisted horror in the years since the Glitch, a constantly starving amalgamation of dying vines, rusting tech, and drooping petals, dotted all over with ever watching, never sleeping eyes. He needs to consume monsters’ souls to support his failing body, as if he doesn’t, the human souls he has left (two have been drained completely, while under his control, and a third is close to shattering) will escape him, and he will literally fall apart.
His mind is just as rotted, a separation and corruption of Flowey and Asriel in one. His Flowey side is absolutely insane and lost to reason completely, while his Asriel side is obsessive, living in the past and consumed by the need to see his “best friend” again. Both sides confuse Aliza for Frisk, and want to both kill and “save” her.
Consuming her soul would restore him to the power he once had with six souls under his command. Everything possible must be done to keep him from getting his vines on Aliza.Flowey has not resided in the Ruins since the early days of the Hunger, once his starvation drove him madder than the Glitch did. He can no longer bear being so close to both the Flower room and Chara's spirit, so he dwells largely in Waterfall, in the deepest swamps, provided with plentiful amounts of prey and water to sustain his monstrous form.