In the Neutral Route, Flowey follows the protagonist throughout their journey after they leave the ruins, watching from a distance. He suddenly appears at the end of game, killing Asgore Dreemurr if the player hadn't already, and steals the six human souls Asgore had collected. Absorbing the souls into himself causes him to transform into a massive, horrifying monster known as Photoshop Flowey who serves as the final boss of the Neutral Route. After the human souls inside of Photoshop Flowey rebel against him, Flowey reverts to normal, allowing the player the choice to kill or spare him before they leave the Underground.

In the True Pacifist Route, Flowey is revealed to actually be the long-deceased son of Toriel and Asgore, Asriel Dreemurr. From experiments with extracted determination in the True Lab, the royal scientist Alphys brought him back to life without a soul as Flowey. The lack of a soul made Asriel incapable of feeling any empathy, turning him from a sweet, caring boy into a bored, violent, and nihilistic sadist as Flowey. Like the Neutral Route, Flowey appears at the very end and steals the six human souls but also steals the souls of every monster in the underground, transforming into a god-like version of his prior self who serves as the final boss of the True Pacifist Route.

In the Genocide Route, Flowey becomes friendly to the protagonist, being open to discussing his exploits and abilities and even recognizing the protagonist as his long-lost sibling. At the very end of the route, after killing Sans and Asgore, the protagonist turns on Flowey. Even after pleading for his life, and revealing his true identity as Asriel in the process, the protagonist violently kills Flowey before ending the entire world.