The new cover of the IDW comic #7 is very interesting, as it shows Twilight sitting majestically on the throne with the three crystals that together make up the Unity Crystals. Ever since the movie it was clear that only she could have been behind the Unity Crystals and this was confirmed by Discord who explained in #2 that the Mane 6 were involved in the creation of these crystals.
But the special MYM was as close to a PR disaster as it could have been, as many people got a violently negative impression of the idea behind the crystals and the fact that the ponies had no magic of their own, and that if they just argued, it would disappear - it becomes a bit too much of coercion and oppression for the sake of “friendship”. The impression is created that the ponies had to be friendly and “kind” in order to keep their magic. Although MYM and later Discord revealed that the magic for the ponies has become deadly, unstable and uncontrolled magic that opens up gaps to unknown dimensions, uncontrolled ripple effects on the environment that can explain many strange animals in the movie and TYT - and that the whole world is put in danger .
The magic had become unstable. And Twilight was unable to solve the problem because MYM showed emotional return from the ponies to the Unity Crystals who then become emotionally hypersensitive. It will mean an intervention in the very essence of the Ponykind. She had to take simultaneous “foci” of the ponies - and possibly the rest of the world - and gather these into a single focus, the Unity Crystals which had become a dam that regulated the magic from the mystical dimension. We don’t know how it works, but all indications are that the active magic in the physical dimension came from another dimension through “foci” in magical beings - as we had discovered in G4, especially when Cozy wanted to take away the magic in S8. And we don’t know what kind of dimension it is. But Discord’s chaos dimension with chaos magic suggests that it may be the dimension where Twilight became an alicorn, meant for pony magic.
The Unity Crystals had become one, which could not be separated with impunity. In MYM, cracks were seen on the earth crystal, as if the dam were about to burst as a result of negative emotions. In the IDW comics it was found that these can be separated without the magic disappearing, and in TYT they act as a kind of on/off light switch. The movie revealed that if they were inactive, you don’t get the magic just by putting them together, as Sunny had discovered. Instead, they were activated by themselves as if they were intelligent and reacted to Sunny`s talk about friendship and the reconciliation of the three pony leaders. This reveals that the Unity Crystals were indistinguishable if the purpose was to take away the magic, and Discord was perhaps the only one in the world strong enough for this, but the magic only weakens for a brief moment. This means that no one is able to remove the magic by simply taking apart the Unity Crystals.
Then it meant that the magic had not been removed voluntarily or as a result of hostile action by an outsider; Sunny and Discord pointed out that there are powerful magical spells that protect the crystals’ integrity and substance. So to take away the magic by disassembling the Unity Crystals - it must be done magically or for the hoof of a “chosen one”. Then it implied that Twilight was responsible for removing the magic for good, throwing the world into chaos.
The cover suggests just such a scenario. The question is, why? Everything suggests that she was forced against her will to take such a drastic step that went against everyone she values. Perhaps an enemy so powerful that she and her friends including Discord had no chance against.