If nine planeswalkers in giant magical mecha couldn't do it, I don't see how any PC's could.
Then again, that was when Phyrexia was whole. Perhaps, after the end of the Invasion saga, it was so heavily damaged, but not destroyed? And, at the heart of ruined Phyrexia, the last diminished shard of Yawgmoth lives, a nothing compared to his old self, but still powerful enough to take over a world if given enough time. and the PC's must go through the ruined layers of Phyrexia, fighting the remnants of the grand armies and the ghosts of the past, to find and finally destroy him.