Spoiler warning for everything.
In Skyward Sword we find out that Demise came forth from underground and invaded. As he dies he curses Zelda, the incarnation of the Goddess Hylia, and Link, the incarnation of the Hero, in a cycle of hatred without end.
What we never find out is: Why did Demise invade?
For answers to this lets look at his incarnations in later games (Ganondorf) as well as how that reflects on other evidence presented in Skyward Sword.
Demise always incarnates as Ganondorf. Sometimes Ganondorf is only partially revived as his demon form Ganon, or sealed as such and escapes that seal later, but he is always born as Ganondorf. Which begs the question: Why choose Ganondorf/become Ganondorf as your vessel?
We know what Ganondorf's motivations are, that he desires to seize control of Hyrule but he has his own reasons for wanting this, he doesn't invade Hyrule in every incarnation simply because Demise is working him like a puppet. This is important because for Demise to incarnate as Ganondorf it would make sense for them to have motives that are in alignment, at no point does Ganondorf just want cooperate with the Hylians only to have Demise seize control of him to force him to take some action he does not want. Based on this we can conclude that the motivations both have are roughly the same so it is logical that those motives originate from the same circumstances. In Wind Waker Ganondorf says:
In Skyward Sword we find out more about the Lanayru Desert and that it was the site where a once advanced ancient civilization mined timeshift stones. We can also see via using the timeshift stones that the desert was once a lush forest environment until it was mined to such an extent that environment was destroyed. This is an accurate representation of desertification (becoming a desert) by mining and it happens in the real world as well when mining processes are abused. The dust smothers plant life at the same time digging disrupts subterranean water flow so the plants can neither drink nor breathe and the constant digging disrupts the roots growing and the soil no longer holds together, furthermore when digging the useless minerals/soil is then deposited elsewhere and becomes a layer of crud that is almost impermeable to water and air so anything underneath it dies. These are grossly abusive mining practices and to use them to the point where a desert as big as the Lanayru Desert is formed means that the ones responsible knew exactly what they were doing and did not care.
The Lanayru Desert also contains an insect named "The Gerudo Dragonfly" which combined with the number of deserts we normally see in a Zelda game (1) pretty strongly suggests the Lanayru Desert and the Gerudo Desert are the same location.
In other words... the people that would go on to become known as the Hylians created the very environment that the Gerudo are born into. Not only do the Hylians not give enough aid to support the Gerudo people but they are also directly responsible for the circumstances that the Gerudo require aid for!
So how does this relate to Demise? It is specifically stated that he came forth from underground, and from a schism in the earth. Logically the easiest place to emerge from underground would be the lowest point on the surface, which in this case would be... the depths of a mine that dug recklessly enough to create a giant desert. That's right, the most logical course of events is that Demise came forth from the depths of the Lanayru mine like a ticked off Balrog.
But that still doesn't really explain why Demise would care about the mining. It doesn't appear that he lived underground as at no point is there any mention of taking the fight to him and forcing him and his armies back underground to their underground civilizations, nor is one ever shown/said to exist. So if Demise and his armies just sprung forth from underground one day and the environment wasn't their concern what could they possibly care about?
How about the most dangerous thing in the history of dangerous things? Time travel. Seriously has no one seen a scifi movie in the Zelda universe? The ancient civilization was using timeshift stones practically every 30 feet and destroyed a massive section of their own planet to get them. Needless to say restraint was clearly not their strong suit. Abusing the timeline in such a manner constantly jumping around in time must have had bigger dangers than just screwing up their own timeline, like degrading the flow of time itself perhaps, which caused Demise to take action.
So Demise invaded to prevent some self destructive morons from dividing by zero. Perhaps he even asked nicely first and explained the dangers but was told by the selfish ancient civilization that they couldn't change their entire way of life based on his complaints, or perhaps he just showed up and was so furious at the damage they were doing to time itself and the environment around them he just started his invasion. Either way from Demise's point of view he was preventing the destruction of multiple worlds from some greedy selfish people playing with powers far too dangerous to be left in their hands and as thanks the Goddesses themselves sided against him and he was sealed and eventually killed. The universe spat in his face and all he was trying to do was prevent its destruction. Now that is motivation worthy of fueling a cycle of hatred without end, and it ties in perfectly with the thoughts of Ganondorf as the leader of the Gerudo.
One last little thing of note is that at the end of Skyward Sword Groose plays a fairly important role in the defeat of Demise and has red hair. It is possible that once Skyloft returned to the surface he settled in Lanayru Desert and his descendants became the Gerudo people and Ganondorf.
-------------------------------------------Impact on the Timeline-------------------------------------------
Everyone seems to think that Zelda is a multiverse because it has multiple timelines, but what if that isn't the natural state of the Zelda universe? If the Zelda Universe was a natural multiverse then whenever there was a situation with multiple outcomes a new universe would form to accommodate those changes. That quickly gets ridiculous to represent accurately as it would result in things such as a universe where Link wears different color boots for a single day or something so it is often simplified in fiction to only major situations with multiple possible outcomes that can create alternate timelines. This means that at the very least every game should create a possible alternative timeline where Link is defeated just like Ocarina of Time did, but they don't.
So, we know alternative timelines can be created but they clearly have a "trigger" that is more than just that moment being super important. It can't just be time travel which causes it because Link travels through the Gate of Time in Skyward Sword to defeat Demise and that is a super important moment involving time travel. Nor can it be the Ocarina of Time because that is used multiple times canonically such as during the Spirit Temple in Ocarina of Time and to prevent the Moon from crashing in Majora's Mask and neither of those events created timeline splits. The case could be made that the timeline split was made the only time Zelda, incarnation of the Goddess Hylia and wielder of the Triforce of Wisdom, used the Ocarina of Time and perhaps that was the trigger but that still doesn't explain the Downfall Timeline as her actions would only have created the Adult and Child Timelines.
So now we're in a bit of a pickle. We've ruled out the timeline splits occurring naturally, and every possible trigger that might have caused it to form reliably. So what if time doesn't like to be split/manipulated? I say "like" but I don't mean to imply that time is sentient but merely that it could have rules which govern it like how heat always flows into colder objects because of entropy (substances able to move will always flow from areas of higher pressure to areas of lower pressure, which is why when you pour out a liquid it doesn't maintain the shape of the cup). Time may very well have a natural flow, like hot to cold and time travel could be the equivalent of forcing cold to flow into hot.
That makes sense right? Previously time could only be altered via powerful artifacts like the timeshift stones and the abuse of which is likely what drew Demise to Hyrule. So it makes sense the timeline split only the one time because its strength was eroded from the constant abuse of time travel combined with the still more time travel occurring and the importance of such pivotal moment in history, but it wasn't simply that specific instance of time travel performed by Zelda which caused the split, rather it was the straw that broke the camel's back as her use of time travel would only have created 2 timelines, but if her use of time travel stressed an already fragile flow of time to the point where it simply fractured into the main possible outcomes of that event, then that is where the third timeline becomes possible, and the only reason we would see a split at that point.
It also explains why in Skyward Sword we see a lot of time travel gone wrong. Time not behaving in a coherent manner as it is being stressed could be seen as a warning sign against the continued use of time travel. Like cracks in a dam.
https://youtu.be/_dnh-0GZkjQ?t=6m58s
But this in turn begs the question of if time doesn't want to be split why wouldn't it flow back into a single timeline immediately? This split into 3 possibilities must have been a violent event for the timestream, creating 3 very different timelines that were too different and didn't have enough in common to combine. Think of it like a wound which needs to heal. From there things only got more different with one timeline flooding, the wars, Link being dead in one of them, Ganon being sealed in one, and Ganondorf being grievously wounded and sealed in another. It would take literally tens of thousands of years for the timelines to become similar enough that the universe could sort of force them together. Think of it this way: Immediately after the split everything was hectic and different, but on a long enough timeline even major events would become minor blips on how large of an impact they had to how things ended up.
Once the timelines were similar enough to combine that might be fine for things all 3 had in common but what about the stuff they didn't? Forcing inconsistencies to overlap should leave some kind of scaring right? Well lets look at the Leviathans. 3 skeletons that each died in 3 different ways, ways which could be considered "extinction level events" that would result in the death of almost everything around them.
A volcanic eruption(Levias' skeleton), a drought(Ocean King's or Jabu Jabu's skeleton), and an ice age(Wind Fish's skeleton). If all 3 of those events happened in a single timeline there probably wouldn't be any survivors, but if each of them happened in a single timeline, like say a drought happened in the Adult Timeline it would make that timeline much closer to the other 2 timelines as Hyrule would no longer be underwater and it makes sense that the casualty of such an event would be the Ocean King or Jabu Jabu. As the Wind Fish is only ever seen in the Downfall Timeline that would indicate the ice age which killed it probably occurred in that timeline and the volcanic eruption must have, by process of elimination, occurred in the Child Timeline. Afterwards we can assume the populations of the worlds would be reduced enough to compensate for the wars and natural disasters that had occurred on each to leave approximately the same amount of people and important historical markers in tact that they were close enough to overlap.
Further evidence of this being the case would be such things as the eighth heroine statue and her sword being so far away, also things like the Forgotten Temple and various other landmarks having their locations "moved" around so that they don't fit any specific timeline. This also tracks with things like Lynels, ChuChus, Lizalfos, and the Rito and Zoras all being present in the same timeline for the first time ever.
-------------------------------------------Metagaming Warning-------------------------------------------
Lastly Nintendo as game developers shouldn't want multiple timelines because in a true multiverse there are no stakes. Why care about a single timeline when they are infinite? And sure having the ability to create a game with any setting is a lot of creative freedom but there is no reason why they couldn't simply make a game with whatever setting they wanted at some point in the timeline they already have as long as they offered some explanation. For example if Nintendo wanted they could flood the world in one game and have the entire world be a desert in the next and a forest in the game after that simply by saying a lot of time had passed or some event had occurred to justify it. Saying "anything can happen at any time because it's a multiverse" isn't creative game making and something a lot of people are not going to be invested in as a narrative.
Let's face it the timeline was created after the fact because for a long time all Nintendo cared about was telling a compelling story in each game and not having those individual stories add up to form any kind of coherent narrative as a whole. That is why we have things like the Master Sword "sleeping forever" at the end of "A Link to the Past" and numerous other contradictions and retcons. As a result it is my belief Breath of the Wild taking place in the Reunified Timeline is Nintendo's attempt to form a single coherent narrative out of all their games which were largely released with the intent to be episodic in nature. They likely changed their stance due to the massive interest of fans in seeing a coherent inter-connected narrative and started working on it with the release of Skyward Sword which laid the groundwork for Breath of the Wild to close that gap and give people a single storyline with real stakes to be focused on and invested in.
In Skyward Sword we find out that Demise came forth from underground and invaded. As he dies he curses Zelda, the incarnation of the Goddess Hylia, and Link, the incarnation of the Hero, in a cycle of hatred without end.
What we never find out is: Why did Demise invade?
For answers to this lets look at his incarnations in later games (Ganondorf) as well as how that reflects on other evidence presented in Skyward Sword.
Demise always incarnates as Ganondorf. Sometimes Ganondorf is only partially revived as his demon form Ganon, or sealed as such and escapes that seal later, but he is always born as Ganondorf. Which begs the question: Why choose Ganondorf/become Ganondorf as your vessel?
We know what Ganondorf's motivations are, that he desires to seize control of Hyrule but he has his own reasons for wanting this, he doesn't invade Hyrule in every incarnation simply because Demise is working him like a puppet. This is important because for Demise to incarnate as Ganondorf it would make sense for them to have motives that are in alignment, at no point does Ganondorf just want cooperate with the Hylians only to have Demise seize control of him to force him to take some action he does not want. Based on this we can conclude that the motivations both have are roughly the same so it is logical that those motives originate from the same circumstances. In Wind Waker Ganondorf says:
So Ganondorf invades Hyrule in each of his incarnations because his people are suffering, and dying. Those he loves and cherishes starve and live poor lives and die of exposure because they live in a desert where nothing grows and the temperatures alternate daily between extreme hots and colds. Meanwhile Hyrule is blessed and prosperous and evidently does not offer aid or as much aid as Ganondorf feels his people deserve.
In Skyward Sword we find out more about the Lanayru Desert and that it was the site where a once advanced ancient civilization mined timeshift stones. We can also see via using the timeshift stones that the desert was once a lush forest environment until it was mined to such an extent that environment was destroyed. This is an accurate representation of desertification (becoming a desert) by mining and it happens in the real world as well when mining processes are abused. The dust smothers plant life at the same time digging disrupts subterranean water flow so the plants can neither drink nor breathe and the constant digging disrupts the roots growing and the soil no longer holds together, furthermore when digging the useless minerals/soil is then deposited elsewhere and becomes a layer of crud that is almost impermeable to water and air so anything underneath it dies. These are grossly abusive mining practices and to use them to the point where a desert as big as the Lanayru Desert is formed means that the ones responsible knew exactly what they were doing and did not care.
The Lanayru Desert also contains an insect named "The Gerudo Dragonfly" which combined with the number of deserts we normally see in a Zelda game (1) pretty strongly suggests the Lanayru Desert and the Gerudo Desert are the same location.
In other words... the people that would go on to become known as the Hylians created the very environment that the Gerudo are born into. Not only do the Hylians not give enough aid to support the Gerudo people but they are also directly responsible for the circumstances that the Gerudo require aid for!
So how does this relate to Demise? It is specifically stated that he came forth from underground, and from a schism in the earth. Logically the easiest place to emerge from underground would be the lowest point on the surface, which in this case would be... the depths of a mine that dug recklessly enough to create a giant desert. That's right, the most logical course of events is that Demise came forth from the depths of the Lanayru mine like a ticked off Balrog.
But that still doesn't really explain why Demise would care about the mining. It doesn't appear that he lived underground as at no point is there any mention of taking the fight to him and forcing him and his armies back underground to their underground civilizations, nor is one ever shown/said to exist. So if Demise and his armies just sprung forth from underground one day and the environment wasn't their concern what could they possibly care about?
How about the most dangerous thing in the history of dangerous things? Time travel. Seriously has no one seen a scifi movie in the Zelda universe? The ancient civilization was using timeshift stones practically every 30 feet and destroyed a massive section of their own planet to get them. Needless to say restraint was clearly not their strong suit. Abusing the timeline in such a manner constantly jumping around in time must have had bigger dangers than just screwing up their own timeline, like degrading the flow of time itself perhaps, which caused Demise to take action.
So Demise invaded to prevent some self destructive morons from dividing by zero. Perhaps he even asked nicely first and explained the dangers but was told by the selfish ancient civilization that they couldn't change their entire way of life based on his complaints, or perhaps he just showed up and was so furious at the damage they were doing to time itself and the environment around them he just started his invasion. Either way from Demise's point of view he was preventing the destruction of multiple worlds from some greedy selfish people playing with powers far too dangerous to be left in their hands and as thanks the Goddesses themselves sided against him and he was sealed and eventually killed. The universe spat in his face and all he was trying to do was prevent its destruction. Now that is motivation worthy of fueling a cycle of hatred without end, and it ties in perfectly with the thoughts of Ganondorf as the leader of the Gerudo.
One last little thing of note is that at the end of Skyward Sword Groose plays a fairly important role in the defeat of Demise and has red hair. It is possible that once Skyloft returned to the surface he settled in Lanayru Desert and his descendants became the Gerudo people and Ganondorf.
-------------------------------------------Impact on the Timeline-------------------------------------------
Everyone seems to think that Zelda is a multiverse because it has multiple timelines, but what if that isn't the natural state of the Zelda universe? If the Zelda Universe was a natural multiverse then whenever there was a situation with multiple outcomes a new universe would form to accommodate those changes. That quickly gets ridiculous to represent accurately as it would result in things such as a universe where Link wears different color boots for a single day or something so it is often simplified in fiction to only major situations with multiple possible outcomes that can create alternate timelines. This means that at the very least every game should create a possible alternative timeline where Link is defeated just like Ocarina of Time did, but they don't.
So, we know alternative timelines can be created but they clearly have a "trigger" that is more than just that moment being super important. It can't just be time travel which causes it because Link travels through the Gate of Time in Skyward Sword to defeat Demise and that is a super important moment involving time travel. Nor can it be the Ocarina of Time because that is used multiple times canonically such as during the Spirit Temple in Ocarina of Time and to prevent the Moon from crashing in Majora's Mask and neither of those events created timeline splits. The case could be made that the timeline split was made the only time Zelda, incarnation of the Goddess Hylia and wielder of the Triforce of Wisdom, used the Ocarina of Time and perhaps that was the trigger but that still doesn't explain the Downfall Timeline as her actions would only have created the Adult and Child Timelines.
So now we're in a bit of a pickle. We've ruled out the timeline splits occurring naturally, and every possible trigger that might have caused it to form reliably. So what if time doesn't like to be split/manipulated? I say "like" but I don't mean to imply that time is sentient but merely that it could have rules which govern it like how heat always flows into colder objects because of entropy (substances able to move will always flow from areas of higher pressure to areas of lower pressure, which is why when you pour out a liquid it doesn't maintain the shape of the cup). Time may very well have a natural flow, like hot to cold and time travel could be the equivalent of forcing cold to flow into hot.
That makes sense right? Previously time could only be altered via powerful artifacts like the timeshift stones and the abuse of which is likely what drew Demise to Hyrule. So it makes sense the timeline split only the one time because its strength was eroded from the constant abuse of time travel combined with the still more time travel occurring and the importance of such pivotal moment in history, but it wasn't simply that specific instance of time travel performed by Zelda which caused the split, rather it was the straw that broke the camel's back as her use of time travel would only have created 2 timelines, but if her use of time travel stressed an already fragile flow of time to the point where it simply fractured into the main possible outcomes of that event, then that is where the third timeline becomes possible, and the only reason we would see a split at that point.
It also explains why in Skyward Sword we see a lot of time travel gone wrong. Time not behaving in a coherent manner as it is being stressed could be seen as a warning sign against the continued use of time travel. Like cracks in a dam.
https://youtu.be/_dnh-0GZkjQ?t=6m58s
But this in turn begs the question of if time doesn't want to be split why wouldn't it flow back into a single timeline immediately? This split into 3 possibilities must have been a violent event for the timestream, creating 3 very different timelines that were too different and didn't have enough in common to combine. Think of it like a wound which needs to heal. From there things only got more different with one timeline flooding, the wars, Link being dead in one of them, Ganon being sealed in one, and Ganondorf being grievously wounded and sealed in another. It would take literally tens of thousands of years for the timelines to become similar enough that the universe could sort of force them together. Think of it this way: Immediately after the split everything was hectic and different, but on a long enough timeline even major events would become minor blips on how large of an impact they had to how things ended up.
Once the timelines were similar enough to combine that might be fine for things all 3 had in common but what about the stuff they didn't? Forcing inconsistencies to overlap should leave some kind of scaring right? Well lets look at the Leviathans. 3 skeletons that each died in 3 different ways, ways which could be considered "extinction level events" that would result in the death of almost everything around them.
A volcanic eruption(Levias' skeleton), a drought(Ocean King's or Jabu Jabu's skeleton), and an ice age(Wind Fish's skeleton). If all 3 of those events happened in a single timeline there probably wouldn't be any survivors, but if each of them happened in a single timeline, like say a drought happened in the Adult Timeline it would make that timeline much closer to the other 2 timelines as Hyrule would no longer be underwater and it makes sense that the casualty of such an event would be the Ocean King or Jabu Jabu. As the Wind Fish is only ever seen in the Downfall Timeline that would indicate the ice age which killed it probably occurred in that timeline and the volcanic eruption must have, by process of elimination, occurred in the Child Timeline. Afterwards we can assume the populations of the worlds would be reduced enough to compensate for the wars and natural disasters that had occurred on each to leave approximately the same amount of people and important historical markers in tact that they were close enough to overlap.
Further evidence of this being the case would be such things as the eighth heroine statue and her sword being so far away, also things like the Forgotten Temple and various other landmarks having their locations "moved" around so that they don't fit any specific timeline. This also tracks with things like Lynels, ChuChus, Lizalfos, and the Rito and Zoras all being present in the same timeline for the first time ever.
-------------------------------------------Metagaming Warning-------------------------------------------
Lastly Nintendo as game developers shouldn't want multiple timelines because in a true multiverse there are no stakes. Why care about a single timeline when they are infinite? And sure having the ability to create a game with any setting is a lot of creative freedom but there is no reason why they couldn't simply make a game with whatever setting they wanted at some point in the timeline they already have as long as they offered some explanation. For example if Nintendo wanted they could flood the world in one game and have the entire world be a desert in the next and a forest in the game after that simply by saying a lot of time had passed or some event had occurred to justify it. Saying "anything can happen at any time because it's a multiverse" isn't creative game making and something a lot of people are not going to be invested in as a narrative.
Let's face it the timeline was created after the fact because for a long time all Nintendo cared about was telling a compelling story in each game and not having those individual stories add up to form any kind of coherent narrative as a whole. That is why we have things like the Master Sword "sleeping forever" at the end of "A Link to the Past" and numerous other contradictions and retcons. As a result it is my belief Breath of the Wild taking place in the Reunified Timeline is Nintendo's attempt to form a single coherent narrative out of all their games which were largely released with the intent to be episodic in nature. They likely changed their stance due to the massive interest of fans in seeing a coherent inter-connected narrative and started working on it with the release of Skyward Sword which laid the groundwork for Breath of the Wild to close that gap and give people a single storyline with real stakes to be focused on and invested in.
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