Sure, Emelious may have that Godslaying sword, but unlike all of the gods that Emelious has killed with it, Sephiroth's plan doesn't involve running into it chest first. In fact, it'll involve the exact opposite, as the One-Winged Angel will take to the skies, giving him an undeniable edge against his ground bound foe. And while Emelious tries to figure out that this flying foe won't crash on his own, despite being in possession of only one wing and all, Seph'll have plenty of time to blow up the sun, then bring down the Shadow Flares upon the godslayer to bag this win.
