Twilight is actually Yawgmoth
- When Twilight gains the power of Harmony and takes over the universe, one of her incarnations manifests in the MTG universe in the form of the Mad Scientist Yawgmoth. Just as Twilight intends to use her power to "cleanse" everything of non-harmonic life, Yawgmoth intends to use the power of Phyrexia to turn everything outside his realm into "perfect beings" under his ineffable rule. And just like Twilight, Yawgmoth is an absolute sadist who enjoys experimenting on anyone who gets in his way, prying away their secrets in the most gory way possible. And just like Yawgmoth, a group of people will band together to bring justice to her horrible atrocities and finally bring her reign of terror to an end.
Twilight will use the following logic as justification to destroy Celestia and Luna.Celestia is day, light, warmth. Luna is cool, dark, night. Both are one of two separate extremes and thus are harmony together, but not harmonious beings onto themselves. Therefor, they are not meant to exist.