I feel like it’s more likely some third party we aren’t privy to yet is responsible.
I think so too; that a third party is involved. From the movie we have received indications that Grogar may be involved, as his bell appears in the scenes, and that collective memory loss seemed to have happened to the ponies. The very heart of Equestria from G4 where the Everfree, Ponyville and the landscape under Canterlot were deserted in the movie.
Also when the glass door appears in the airship station; the Unity Crystals were not united. They were shown separately, and the lighthouse seemed to have never been used as a place for the Unity Crystals. Sunny ponders whether the Unity Crystals were united and that these were separated because the magic had become uncontrolled, that was what she suggests 3.59 in the last trailer - and she does not like this speculation. Zipp looks accusingly at the Unity Crystals 3.58, which suggests she is not comfortable with her discovery. At the very least, the Mane 5 is in line with us about the unpleasant information about emotional instability on magic, and that all magic comes from the Unity Crystals themselves.
We know that Twilight Sparkle probably created the Unity Crystals, as her cutie mark is attached to it, and that it may be her masterpiece that may have been developed at the height of a time of greatness when friendship and harmony were spread throughout the world. But it seems that it is not without faults; the earth ponies`s hooves were to be lit up as with the wings of the pegasi and the horns of the unicorns, when the magic was released. It did not happen; instead, it looks like the magic was “turned off” in the earth ponies, and this leads to corruption in the crystal of the earth ponies who then crack.
It is possible that pony magic may have become unstable not only because the ponies began to fight with each other, but also because the magic itself had become erratic. There were several chimerian small animals that we have seen on TVT, including raccoons and others with horns and wings, such as the “flying snails” that we know did not exist in the old G4. As if they were exposed to uncontrolled and erratic magic.
I remembered a special where the Mane 6 in G4 came across pale ponies in a village, giving them back the colors as soon as they were emotionally uplifted with positive emotions. This was one of several examples where the human authors thought the ponies’ utopia should be based on “be kind and happy, otherwise -!”
But now over to the matter; the state that the harmony tree was in when it was discovered in the movie, may indicate that it was in the Ground Zero when the magic completely disappeared in Equestria once in the past. SOMEONE had wiped out the entire area around the tree, not even the ruins of the two sisters’ castle are back. As if a nuclear explosion or a magical explosion had happened.
Furthermore, it has been revealed that the dragons had not appeared for “several generations”, at least a couple of centuries, so that means they stay far away from Equestria and would have nothing to do with the ponies. The existence of the dragon egg shows that the dragons are still in existence. This may be the case with all non-ponies who may have fled the ponies for reasons we do not understand.
Could it be that the pony magic had become unstable and a danger to the environment due to the emotional impact that in the end may have become too much? But the pony magic had been stable and part of the background magic for thousands of years. We know that the ponies did not exactly live in deep harmony with each other in their old homeland, and the windigos provoked the catastrophe rather than let it happen by itself.
The ponies then have to live with magic when the special is over, but a seed of doubt is planted, would it be better to live without magic, when one is safe from erratic magic, than to live with magic that can become one’s own enemy without warning?
Here Sunny and her friends have to go to the bottom to solve this dilemma. And we may have a possible motive for Discord when he stole one part of the Unity Crystals, not just out of grief or fear of outside threats.
The whole matter of the lost magic becomes more enigmatic, now that it is revealed that the pony magic can be very dangerous for the ponies.