This theory was in thanks to my friend Atnok for explaining to me how it could be that in Season 2, "Return of Harmony Part 1" that Celestia could say "Discord is the mischievous spirit of disharmony. Before my sister and I stood up to him, he ruled Equestria in an eternal state of unrest and unhappiness. Luna and I saw how miserable life was for Earth ponies, Pegasi, and unicorns alike, so after discovering the Elements of Harmony, we combined our powers and rose up against him, turning him to stone.", the line "after discovering the Elements of Harmony, we combined our powers and rose up against him, turning him to stone." stood out to me.399Please respect copyright.ＰＥＮＡＮＡrXaaeMo8cD
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        Why? Because in Season 7, "Shadow Play" Star Swirl, after seeing the map, says "Something about this magic seems familiar..." before he zaps it and realizes it is magic from him and his comrades. He then refers to the tree they grew in this manner "More importantly, we no longer need Ponhenge to send our foe back to limbo. We can use the stored magic in this Tree of Harmony.", saying "in this Tree of Harmony" not "in the Tree of Harmony" as if it is but merely an object for use. True it is but he doesn't listen to Twilight's warning about how the land would be in danger should the tree die, since in Season 4, "Princess Twilight Sparkle" we see without the tree's magic the Everfree Forest goes wild. (Even though those vines were from the plunder seeds, the tree keeps them at bay thus under control)399Please respect copyright.ＰＥＮＡＮＡafC6MBIRUj
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        So if Star Swirl never knew about the tree and wasn't around to show Celestia it before his being trapped in limbo, since he didn't even realize the seed had grown over the years, how would she had found anything on the Elements of Harmony and where to find the Tree of Harmony? He wouldn't had been able to release a book or take notes and send them to the old castle for her to find after his banishing spell.399Please respect copyright.ＰＥＮＡＮＡDHQUrQnylF
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I'm sure we all recall the wasteland Twilight showed Starlight in Season 5, "The Cutie Re-mark" and how Starlight denied that future coming true. I've heard in videos the theory that all the villain's came back at once and destroyed everything. But, what if it wasn't all the villain's that destroyed all life from the land? What if it was a single villain that we had only heard mentioned once and did not see until Season 7, "Shadow Play"?399Please respect copyright.ＰＥＮＡＮＡLVm8147RSn
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        Yes, I am proposing the theory it was the Pony of Shadows that caused the mass end to all life from Equestria to result in the gloomy wasteland we saw. It is said by Star Swirl to Twilight's concern for the tree, "If the Pony of Shadows has his way, your land will not exist. So unless you have a better idea..." and what better way to do that than to destroy literally everything, since even some of the villain's could have a fragment of good in them towards someone or something.399Please respect copyright.ＰＥＮＡＮＡ3jNpJ44Vc8
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So now I will be explaining how what Celestia said back in Season 2, we saw in Season 4 from Zecora's potion and what was displayed in Season 7 with Star Swirl all adds up while it still knocks out what Journal of the Two Sister's told us.399Please respect copyright.ＰＥＮＡＮＡctpHKH5Dsj
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> The wasteland was caused by the Pony of Shadows399Please respect copyright.ＰＥＮＡＮＡptsnkjLPdU
- The Pillars had the Pony of Shadows trapped for over a thousand years, using their magic never ending to sustain the sealing spell for limbo399Please respect copyright.ＰＥＮＡＮＡgZqOIjLWBs
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- When the Pillars were returned, all were dazed and exhausted with Star Swirl lacking magical power399Please respect copyright.ＰＥＮＡＮＡ6DQAUHTNRG
- - It seems more reasonable that his magic was running low with the others and sooner or later it was going to fail, Twilight just sped up the process with her spell399Please respect copyright.ＰＥＮＡＮＡ2t5dChdfUu
- - - This could also play into that actually being the Pony of Shadows at the castle of the Royal Sister's back in Season 4, "Castle Mane-ia", if Star Swirl's spell was weakening. It could have also been Star Swirl spying while the Pony of Shadows was spying. I say this because Twilight never told him she had studied his writings outside of the reading of his journal. Yet he says to her "You have studied my writings. Surely you have some other plan.". How else would he had known she had studied his works besides his single journal if not for spying once or twice while Twilight was in the old castle? Some of those books must have been his that had never been moved to Canterlot and we know she has read some of the books in there.399Please respect copyright.ＰＥＮＡＮＡeTGypYkfxC
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- When Starlight was messing up the time line to keep Twilight from meeting her friends, this would strongly imply the elements were likely never returned to the tree since Celestia would probably use them when she could when needed399Please respect copyright.ＰＥＮＡＮＡxQayJByw5A
- - Celestia keeping the elements would ensure she could use them from time to time, even if it strains her greatly, to take out the villain's we've seen or renewing the banishment spells on them399Please respect copyright.ＰＥＮＡＮＡCNmtoJcLbQ
- - Celestia possibly could have kept Discord as stone easier if she kept the elements in use when she could muster enough magic to use them. This would make him easy pickings for the Pony of Shadows because if one is stone and broken, wouldn't that result in their death?399Please respect copyright.ＰＥＮＡＮＡ7CokWyyxFl
- - If Celestia kept the elements and had no student under her wing to take over the elements, Starlight would never had been found and reformed, Sunburst would have stayed reclusive from others and would never had gone to the antique store with Twilight and Starlight. Thus Sunburst would have never bought the barrel with Star Swirl's journal in it which spoke about the Pony of Shadows and when taken to Ponhenge, would never show anyone what went down there all that time ago.399Please respect copyright.ＰＥＮＡＮＡIdV7TB9jRF
- - - Without this knowledge, Celestia probably wouldn't be expecting the Pony of Shadows to return if she thought it had been destroyed due to its extended absents. Not expecting it she wouldn't be able to ready the elements before the Pony of Shadows could use his magic to cast his darkness across the land. Even if she had a brief vision like she did with Teirk, who would she send to locate the moving threat? She wouldn't have Twilight nor the use of Discord who would still probably be stone and no Luna who would also probably be stuck in the moon.399Please respect copyright.ＰＥＮＡＮＡv6MwzyU6E4
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> Celestia knowing about the Tree of Harmony and Elements of Harmony without giving out the knowledge of Star Swirl telling her about them399Please respect copyright.ＰＥＮＡＮＡmIYUqlmFrN
- Along the time line where the result was a wasteland of nothing, no one would likely have been trying to figure out what happened to the Pillars or the Pony of Shadows which would result in Star Swirl eventually losing hold on the spell. The Pony of Shadows escapes and upon that, the exhausted Pillars hide to try recovering and try to beat him but end up failing. Before the epic failure, Star Swirl flees with the group shielding him since he is the strongest with his magic. He runs to where they planted the seed and finds the Tree of Harmony in this falling future.399Please respect copyright.ＰＥＮＡＮＡRX0cuuNO7F
- - He could, in theory, put his horn to the tree and focus since the time line was out of whack and use magic to travel back into the past before sealing the Pony of Shadows. This would be to tell Celestia about the Tree of Harmony and of the elements as well as a theory for how they work. (I figured he would be able to put two and two together based on branches and the number of empty slots) He tells her to only seek them out and use them with her sister when their powers alone fail to defeat an evil. (Also figuring he would see the withered state of the tree without the elemental stones and figure they needed to be there to recharge the tree)399Please respect copyright.ＰＥＮＡＮＡ8kZVHC4ARW
- - Celestia agrees but before she can question him further he vanishes, the future him disappearing as the past him is sealed away with the others into limbo. Celestia would, I am assuming, take his vanishing as a teleportation spell thus leaving her with questions about where he went and what happened.399Please respect copyright.ＰＥＮＡＮＡhh3ggrkhl1
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- In doing this act it helped mend the time flow for the time being so when Rainbow did her sonic rainboom, Twilight and Starlight returned to how things were before the time spell was used by Starlight399Please respect copyright.ＰＥＮＡＮＡdMYU718hwv
- - In the flow being fixed, Celestia would know inside that Twilight would be able to release and use the elements properly to their full potential while retaining the knowledge of the tree and elements, even if she either doesn't recall Star Swirl telling her it or decided to not reveal Star Swirl told her about them in advanced399Please respect copyright.ＰＥＮＡＮＡnzelF79gUx
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> Star Swirl not knowing about the tree or the elements399Please respect copyright.ＰＥＮＡＮＡSXyeRlBXbT
- In using the magic left in the tree to go back in time, Star Swirl from the wasteland future would give the information about the tree and what the elements should be able to do to Celestia before he vanished399Please respect copyright.ＰＥＮＡＮＡaNv7xVtYgR
- - With the time flow fixed, the future Star Swirl that fell out of limbo due to lack of magic to maintain the spell would no longer exist because that future would no longer exist399Please respect copyright.ＰＥＮＡＮＡOwZRjQBb4e
- - Without the wasteland being a future, Star Swirl in the present in limbo wouldn't remember an event that never happened. He would not remember his and their magic running out or low enough to allow the Pony of Shadows full freedom. He wouldn't remember watching or seeing the land fall into devastation that was void of life. He wouldn't remember seeing the tree and going back in time to tell Celestia about what would form later on in the Everfree. All this because none of that happened yet once the time line was put back to normal399Please respect copyright.ＰＥＮＡＮＡwvthSqYmh1
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- With his spell being broken before it ran out or before the Pony of Shadows could break free from their slowly weakening states, Twilight prevented the wasteland future from becoming true since she intervened before the threat could come back without much notice399Please respect copyright.ＰＥＮＡＮＡb6diyePzVe
- - This interfering ensured Star Swirl wouldn't recall a future that had yet to happen since the elements were back with the tree, keeping it strong and with the main six's alternative fix, prevented the possibility of the wasteland reoccurring399Please respect copyright.ＰＥＮＡＮＡTx9pTDuZMI
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I'm aware this sounds like a huge leap but given how Twilight herself as messed with time once and Starlight messed with time much worse than Twilight, I wouldn't put it past that wasteland event happening with Star Swirl's return to bring about Celestia knowing about the tree and elements. A tree and elements that weren't even grown yet when the Pillars banished the Pony of Shadows since they planted it before casting that banishing spell at Ponhenge. If this couldn't possibly be probable then how would you explain Celestia knowing about the elements and the tree, as well as how to use them when facing Discord when later on we learn Star Swirl vanished before the tree grew, thus knew nothing of the seed actually sprouting into a mighty force of hope and light.399Please respect copyright.ＰＥＮＡＮＡTm9ksnFRC4
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    Also, remember this exchange?399Please respect copyright.ＰＥＮＡＮＡRPa5Pre8PZ
    Twilight Sparkle: But you can't stop me from trying, and we could be stuck doing this for all eternity!399Please respect copyright.ＰＥＮＡＮＡ5XOlCQy8Hr
    Starlight Glimmer: If that's what it takes to keep you and your friends from getting your cutie mark connection, then I'm game!399Please respect copyright.ＰＥＮＡＮＡkivoSSefh5
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    Given how fickle time travel is, couldn't a loop from previous be probable until it finally ended with Starlight allowing the rainboom to happen?399Please respect copyright.ＰＥＮＡＮＡuf1Jus1K3q
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