Board Thread:General Discussion/@comment-27907368-20160506131212/@comment-4383275-20160827033314

Flowey's message at the end of the True Pacifist Run may certainly have been deceptive, as he's shown to be a master manipulator throughout the game. From his introductory sequence to the way he messed around with Papyrus throughout the non-Genocide playthroughs of the game to, of all things, the way he makes a big show of trembling before Frisk/Chara in the Genocide Run when he's about to die (after all, he can't actually feel fear because he's soulless and, therefore, emotionless), Flowey seems to know just how to pull everyone's strings.

Moreover, Flowey's aptitude for manipulation is explained by his monologue in the Genocide Run: "'I've done everything this world has to offer. I've read every book. I've burned every book. I've won every game. I've lost every game. I've appeased everyone. I've killed everyone. Sets of numbers... Lines of dialogue... I've seen them all.' But you... YOU'RE different. I never could predict you." Flowey represents the player who's replayed Undertale so many times that they have nothing left to do but turn to the Genocide Run, so clearly, he must know how to make any character act how he pleases.

But.

Even with this, Flowey could never harm the True Pacifist timeline. As Asriel, he wants the player dead in order to take control of the timeline, but he can't override the player's SAVE file, as proven by his quote: "''Your DETERMINATION! Somehow, it's even greater than mine!" ''It's not clear if he's addressing Frisk, Chara, or the player, but he uses the name that the player has given to the fallen human.

Conclusion: Flowey wants to reset the timeline in the True Pacifist Run but knows he can't, so he begs the player to leave so he can have, at the very least, some desparate chance to claw at his dream of controlling the timeline.