I've been thinking about how the underground, sky, and surface all play into each other, piggybacking off Kevin's post from earlier about restoring the Sky kingdom. My speculation is after Ganondorf reawakens due to the seal being broken, he spreads Malice throughout the Hyrule underground which seems into the surface and wreaks havoc, and either he or the deity reveals the cloud barrier.
Link is taken up to the Sky Kingdom ruins to recuperate from the Malice attack, obtain his new gauntlet and be informed by either the deity (spirit arm), Zelda, or some other NPC that because of Ganondorfs Malice weakening the magic seal, pieces of the Sky Kingdom ruins have fallen to the surface.
Link is able to use the new rune to reverse the flow of time of an object, and can use it to pull chunks of the islands back up. Once the ruins of a certain area have been put together, he can use a more powerful version of that ability to rewind it to a previous ancient state, which may end up being a new location like a dungeon, city, or landmass with shrines. Within this could be green energy which can combat Malice, possibly in a highly concentrated and potent 'teardrop'.
Link can then use his surface phasing rune to dive underground, or he can pull chunks of Hyrule to the Sky to reveal caverns going underground. By entering these underground passages he could destroy a Malice "nest" (I'm thinking Doom) with a partially restored Master Sword or green energy.
Progression could be determined by ridding the land of Malice and restoring the original Sky Kingdom. I also think Ganondorf will attempt to resurrect himself to his original living body, and will get more difficult the longer you take to reach him since he's further along his resurrection.
But also I have so many questions, like why Ganondorf was even kept around in the first place under Hyrule Castle generating Malice. Was it to prevent his reincarnation? Or is something sinister going on?Calamity Ganon seems to have been a puppet the whole time.
(I need to go to bed)