Some of these have more obvious answers, some can be answered with a little speculation, some require a lot, and some are just unanswered.
I just replayed.
Anyway, something isn't adding up.
Either Nintendo is just sort of sloppy, or there's a mystery here. At the very least, it doesn't make sense why Hylia's own plan A of becoming mortal to wish on the Triforce didn't work. Then it doesn't make sense why plan B of Link wishing on the Triforce was even necessary when plan B was making Link powerful enough to defeat Demise. This theory is complete, but it makes as many speculations as any other.
THE BORING THEORY:
The Master Sword is in skyview temple all along, just the pedestal is lowered in the ground until the ending. The Imprisoned lacks Demise's consciousness theory, which is what it hopes to obtain at the Skyview Temple. The Tree of Life follows timeshift stone rules because that's how you obtained the seedling. If you had obtained the seedling by going into the Time Gate, it would have followed "it's always been that way" rules.
The problem with this theory is that while it's tidier than others, it still relies on speculation that is not confirmed in any way. We have to assume this theory that the Imprisoned is Demise's brainless essence, but that's just made up speculation, although a point was made to tell use Demise's consciousness was in the sword. Still, we are told the imprisoned is after the timegate to destroy it, then he's after Zelda. But maybe that's plot misdirection where we imagine he was after his consciousness in the hidden sword the whole time.
The strongest evidence against this theory is the seal on the Imprisoned. There's no reason to think "Demise's essence slowly returned and Impa created a new seal and resealed it". That is purely speculative. As far as we know, the sealing spike was put there by Hylia.
So how do we return from defeating Demise in the past, and find that the temple and Triforce defeat of Demise is something that still happened in the future. That's the strongest evidence for two timelines.
ANOTHER THEORY:
Zelda going through two separate gates creates a paradox, splitting the timeline. One where Impa does vigil over the Master Sword and the Skyloft future never happens, but Demise is defeated already. I don't know how this works, but remember that Zelda never returned back through the Lanayru gate. She came to the future by waiting. So she never reset to her own proper timeline. I don't know if that would affect going through the Skyview gate.
When Zelda and Link return, they return to the old "I stood vigil over the crystal" timeline where Demise was only just defeated. This assumes the Impa which saw Link first open the Skyview gate was crystal Impa (she was for a while). She's still crystal Impa when they return. They only defeated Demise in Ghirahim's second chance timeline. Sword Impa becomes an orphaned timeline where the Skyloft events happen differently or never happen.
There's only one thing needing explanation: the Master Sword. Whatever could have created a second Master Sword could also explain Impa's bracelet. As if crystal Impa didn't experience Sword Impa's timeline, but somehow Sword Impa managed to get the sword and the bracelet across the multiverse to her for some reason.
The only way there's room for this theory is looking at Hylia's plan A to wish on the Triforce herself, which we never see happen, and which Demise hints at by referencing how she had to become mortal to seal him. So this implies a kind of conspiracy or secret to create a second timeline but conceal it.
GRAND HYLIA CONSPIRACY OF TIME THEORY:
Demise is said to be "the eternal being who has conquered time itself and the source of all monsters". How do you defeat a being who has conquered time? What did Fi mean he had conquered time?
I have a little theory that the Downfall timeline Ganon, the one who obtained the Triforce, found a way to become Demise and loop himself back in time. Ensuring his inevitable existence.
In this theory, the "Demise is defeated in the past" timeline becomes the three split timelines of Ocarina of Time.
The "Demise is defeated by the Triforce in the future" timeline becomes the BOTW/TOTK timeline.
The idea is that the three split timelines allow for Ganon to always win in one timeline enough to go back in time and ensure his own creation. He cannot be purged from time.
My theory also has the Child Timeline Master Sword split into a sword of light and a sword of darkness. The sword of darkness would be obtained by downfall timeline's ganon to become Demise (I assume an additional Triforce wish was used that sends Demise back to the beginning of time, and his demon realm is then what Din or the Oocca build Hyrule's surface on top of to seal the demon realm
The sword of light might be what is brought back secretly to the original Skyward Sword timline at the finale to become the BOTW Master Sword.
So Hylia's god-level strategy for defeating this demi-god who "conquered time itself" is to branch a secret timeline that can loop around and seal Ganon/Demise in his own loop of inevitable defeat, and give Hyrule a future without him.
If that TotK situation is part of a plan by Hylia, then perhaps somehow it's the result of her Triforce wish which Skyward Sword never reveals. Link is then given the resources to use the Triforce to defeat Demise in the Skyloft timeline, before being prepared to go back in time to the Master Sword timeline to defeat Demise there. This tricks Demise who is not aware of the other timeline, and it's why he's safely caught in the OOT three timelines -> Skyward Sword loop.
Yeah I know, nutso theory. But it almost works. Why didn't Hylia as Zelda just wish on the Triforce herself? Wasn't that plan A? So it feels like there was a wish and the game is deliberately hiding it from us. Then the bracelet and Master Sword at the end become these contradictions along with the Tree of Life, like elephants in the room.
I suspect that Nintendo had planned that after you get the Master Sword in Skyward Sword, you go to the past and there would be past versions of the lands to explore, in the quest for the Triforce, but it was cut content. If they had done that, having a separate Zelda and Link plan makes more sense. But they never cut the two plans storyline.
Still, it's a huge hanging plot thread. Hylia becomes mortal to wish on the Triforce. But we never see that. Link wishes on it, and defeats Demise with the Master Sword. Demise has to be defeated twice. That's weird.
I just replayed.
- Why does Impa have Zelda's bracelet at the beginning, but the Tree of Life and Master Sword aren't there yet?
- Why does Zelda say Hylia made two different plans? As if each alone could solve the problem. The first plan is Fi and Link, which I assume goes all the way to the TriForce since you use the sword to access the sacred realm. The second plan is to become mortal specifically so Hylia can make a wish on the Triforce
- Why does Demise say, "You gave up your immortal form to imprison me." I feel like we never saw that happen in the game, but Demise is referencing it as if he has seen it.
- Why did Zelda awaken her memories and go to the past? Why did she sleep? She explains this as she has to "maintain the vigil of Hylia to keep Hylia's seal on the Imprisoned". But she doesn't have to be mortal to do that.
- What is with the silent realm? What is Link doing there with the spirit flower?
- What does Zelda's blessing of the master sword accomplish? If she's mortal, how does she do this (I assume this is just the generic power of light in all the Zelda's lineage which must once have belonged to Hylia)
- Why collect the flames of the goddesses, and what are these relative to the triforce?
- Why collect the flames AND the song of the hero as part of the quest? Why not just get the flames and the master sword unlocks the Triforce?
- Why have the Triforce be used so late after the plan was made? Did it have to recharge?
- Other than Zelda having a crush on him, what in particular makes Link the "chosen hero". Yes he went through spirit trials and gained godly power, but Demise says his swordsmanship is unlike any god or man he met. I assume this means something to the effect that the trials Link went through and the power he obtained (the game's main story) took him up to that level. This is how he was part of the plan.
- If Demise was killed in the past, then why would Link have wished the Sealed Temple to fall on him? Wouldn't that have not needed to happen?
- "It's all like the timeshift stones, they violate causality." Then why did Impa have Zelda's bracelet from the getgo???
- Hylia had two plans. The main story is only the Fi/Link plan. Hylia's own Triforce wish is a secret.
- There are two time gates. The sealed temple time gate very much seems like a secret back-up plan, and is very much associated with the Master Sword. So it's likely connected to the chosen hero plan, which therefore probably involves giving the chosen hero a path to the past to defeat Demise at the time of the seal breaking. The main plan, therefore, would be to use the temple of time to become mortal and go back to use the Triforce on Demise. Or something like that.
Anyway, something isn't adding up.
Either Nintendo is just sort of sloppy, or there's a mystery here. At the very least, it doesn't make sense why Hylia's own plan A of becoming mortal to wish on the Triforce didn't work. Then it doesn't make sense why plan B of Link wishing on the Triforce was even necessary when plan B was making Link powerful enough to defeat Demise. This theory is complete, but it makes as many speculations as any other.
THE BORING THEORY:
The Master Sword is in skyview temple all along, just the pedestal is lowered in the ground until the ending. The Imprisoned lacks Demise's consciousness theory, which is what it hopes to obtain at the Skyview Temple. The Tree of Life follows timeshift stone rules because that's how you obtained the seedling. If you had obtained the seedling by going into the Time Gate, it would have followed "it's always been that way" rules.
The problem with this theory is that while it's tidier than others, it still relies on speculation that is not confirmed in any way. We have to assume this theory that the Imprisoned is Demise's brainless essence, but that's just made up speculation, although a point was made to tell use Demise's consciousness was in the sword. Still, we are told the imprisoned is after the timegate to destroy it, then he's after Zelda. But maybe that's plot misdirection where we imagine he was after his consciousness in the hidden sword the whole time.
The strongest evidence against this theory is the seal on the Imprisoned. There's no reason to think "Demise's essence slowly returned and Impa created a new seal and resealed it". That is purely speculative. As far as we know, the sealing spike was put there by Hylia.
So how do we return from defeating Demise in the past, and find that the temple and Triforce defeat of Demise is something that still happened in the future. That's the strongest evidence for two timelines.
ANOTHER THEORY:
Zelda going through two separate gates creates a paradox, splitting the timeline. One where Impa does vigil over the Master Sword and the Skyloft future never happens, but Demise is defeated already. I don't know how this works, but remember that Zelda never returned back through the Lanayru gate. She came to the future by waiting. So she never reset to her own proper timeline. I don't know if that would affect going through the Skyview gate.
When Zelda and Link return, they return to the old "I stood vigil over the crystal" timeline where Demise was only just defeated. This assumes the Impa which saw Link first open the Skyview gate was crystal Impa (she was for a while). She's still crystal Impa when they return. They only defeated Demise in Ghirahim's second chance timeline. Sword Impa becomes an orphaned timeline where the Skyloft events happen differently or never happen.
There's only one thing needing explanation: the Master Sword. Whatever could have created a second Master Sword could also explain Impa's bracelet. As if crystal Impa didn't experience Sword Impa's timeline, but somehow Sword Impa managed to get the sword and the bracelet across the multiverse to her for some reason.
The only way there's room for this theory is looking at Hylia's plan A to wish on the Triforce herself, which we never see happen, and which Demise hints at by referencing how she had to become mortal to seal him. So this implies a kind of conspiracy or secret to create a second timeline but conceal it.
GRAND HYLIA CONSPIRACY OF TIME THEORY:
Demise is said to be "the eternal being who has conquered time itself and the source of all monsters". How do you defeat a being who has conquered time? What did Fi mean he had conquered time?
I have a little theory that the Downfall timeline Ganon, the one who obtained the Triforce, found a way to become Demise and loop himself back in time. Ensuring his inevitable existence.
In this theory, the "Demise is defeated in the past" timeline becomes the three split timelines of Ocarina of Time.
The "Demise is defeated by the Triforce in the future" timeline becomes the BOTW/TOTK timeline.
The idea is that the three split timelines allow for Ganon to always win in one timeline enough to go back in time and ensure his own creation. He cannot be purged from time.
My theory also has the Child Timeline Master Sword split into a sword of light and a sword of darkness. The sword of darkness would be obtained by downfall timeline's ganon to become Demise (I assume an additional Triforce wish was used that sends Demise back to the beginning of time, and his demon realm is then what Din or the Oocca build Hyrule's surface on top of to seal the demon realm
After which point it becomes the Depths and it is from here Demise breaches.
The sword of light might be what is brought back secretly to the original Skyward Sword timline at the finale to become the BOTW Master Sword.
So Hylia's god-level strategy for defeating this demi-god who "conquered time itself" is to branch a secret timeline that can loop around and seal Ganon/Demise in his own loop of inevitable defeat, and give Hyrule a future without him.
In TotK: Ganon is totally defeated. While no reference is made to Skyward Sword or Hylia, the plot involves a time loop with Zelda that guarantees Link will have the resources to defeat Ganon. The symbol in the game logo is an Ouroboros, heavily implying that the loop of time Zelda is in is part of what enables Ganon's defeat.
If that TotK situation is part of a plan by Hylia, then perhaps somehow it's the result of her Triforce wish which Skyward Sword never reveals. Link is then given the resources to use the Triforce to defeat Demise in the Skyloft timeline, before being prepared to go back in time to the Master Sword timeline to defeat Demise there. This tricks Demise who is not aware of the other timeline, and it's why he's safely caught in the OOT three timelines -> Skyward Sword loop.
Yeah I know, nutso theory. But it almost works. Why didn't Hylia as Zelda just wish on the Triforce herself? Wasn't that plan A? So it feels like there was a wish and the game is deliberately hiding it from us. Then the bracelet and Master Sword at the end become these contradictions along with the Tree of Life, like elephants in the room.
I suspect that Nintendo had planned that after you get the Master Sword in Skyward Sword, you go to the past and there would be past versions of the lands to explore, in the quest for the Triforce, but it was cut content. If they had done that, having a separate Zelda and Link plan makes more sense. But they never cut the two plans storyline.
Still, it's a huge hanging plot thread. Hylia becomes mortal to wish on the Triforce. But we never see that. Link wishes on it, and defeats Demise with the Master Sword. Demise has to be defeated twice. That's weird.