I want to give my theory based on both Misty’s story and Twilight’s recording. But first I want to put threats to Equestria and how they’re dealt with into perspective, in a slightly tongue-in-cheek way.
Celestia and Luna: Seal it away so someone else can deal with it.
Celestia: Just hope that nothing threatens Equestria.
The Mane Six: Have Equestria pushed to the brink of disaster, figure out which virtue causes this special’s Deus Ex Machina to proc and defeat the villain, then basically forget about it.
Anyways, here’s where my theory is at:
Misty’s statement about how most of Equestria’s magic belonged to Opaline contains a kernel of truth. At her original strength, Opaline was one of the most powerful beings Equestria had ever faced, and she had set her sights on Equestria’s magic.
Whatever Opaline was going to do to steal the magic, Twilight found a way to turn it against her, leaving her drained. “Magic is more powerful than its ever been” because of this.
The crystals were created to keep this newfound power under control and out of the hooves of Opaline. The Barrier was also created to keep Equestria hidden.
Twilight recorded her message after the barrier failed.
So to put Opaline in perspective (if I’m correct):
Twilight when Opaline shows up: Drain her power, seal it in magical artifacts that not even Discord can destroy, put up a barrier around the entire kingdom, then warn future generations that that’s probably not even enough to stop Opaline.
It has been noted in TYT ep. 29 that Opaline is not “a being of fire” but a fire alicorn. This in itself is startling, because all alicorns in G4 are loosely defined as little more than what they are, normal alicorns if that word can be used. Celestia, Luna, Cadence and Twilight are characterized by their magical specialty - sun, moon, love, magic, and each individual alicorn is thus unique. But Misty’s remark more points to a specific alicorn group, as “water”, “earth” and fire” for example. An individual alicorn cannot be described as a fire alicorn if she is unique like the other G4 alicorns.
Also, Opaline had demonstrated in E8 that she is capable of assimilating magic - and it seems that she reacted particularly to fire magic, such as dragon fire. She obviously couldn’t assimilate normal magic because if that’s correct, she would have gone into a Tirek beserk gait after the magic returned. However, she requests certain magic that seemed to originate in the creation of fire as seen with the lantern that Misty tried to steal and then the bottle of dragon fire, which she was able to salvage. Opaline was desperate to get hold of the baby dragon.
We still don’t know where she came from. G5’s problem now is that there are too many drummers on the same drum, who do not communicate well with each other. That’s why we see a lot of weird and wrong between the G5 movie, the TYT, the MYM and most recently the IDW Comics. It creates a lot of mess, and in many places it drags down the quality or creates controversies that no one is ready to process.
With a little goodwill, it is possible to put the pieces together using lore from all mediums. We first saw Opaline in MYM C1, and her appearance was correctly shown in IDW G5 #2, as “censored” so we didn’t see which pony she was. This took place after the last episode of S9. In E2 we learned about the threat she poses, that she wanted to steal all magic and almost succeeded. But Twilight also said that Opaline had plans to “open” something undefined. In E6 we learned that Twilight took her magic and put it in the crystals. In the movie we learned that the crystals existed in peaceful times when Equestria had magic, so Sunny’s conclusion is not correct.
Discord knew Opaline, he was somewhat sarcastic in his tone when she was mentioned. If the IDW comics are not too far from the others, it is obvious that the Mane 6 could not stop the development where the magic starts to run wild, as seen in MYM C1 and partly C2 E2. They had to deal with unstable magic, hysterical ponies who may have been thrown into a conflict of interest between rival alicorns, and a dangerously evil alicorn who showed no signs of being corrupt. When Twilight made the Unity Crystals, it was based on a book about alicorn magic. Likely to strip Opaline of her alicorn magic. But they also had to “fix” the problem of unstable magic, and all magic had to be collected to bring order back to Equestria. I think MYM writers fumble a bit here because they couldn’t avoid unnecessary details without deleting it completely.
Opaline was led away in chains, possibly placed under house arrest in the dark castle. The information that Twilight had erected a barrier to hide Equestria is either a mistake or a result of a lack of insight into the lore from the G4 when the work was going on. Because if Opaline was stripped of her magic and put under house arrest, why would Twilight go to such extremes?
It’s as if the writers of MYM have only seen S1 of G4 and ignored the rest, especially Twilight’s strong interest in international stability as a result of the Storm King’s attack, in S8-S10. After all, the last seasons revealed that Twilight was very interested in the world outside of Equestria. The G4 movie paved the way for this. It would be logical that the barrier is of the same type as the one that surrounded Brighthouse, i.e. invisible to everyone except those who use magic to spy. Or that it’s there after Equestria’s collapse to protect the ponies from the rest of the world. So the writers must save the situation by changing this, immediately!
If the barrier was there while the active magic was gone, it means that Opaline who may have been on the loose after Equestria’s collapse was able to use magic. We know that the Unity Crystals were magically active at the same time. So the alicorn magic is immune to the Unity Crystals, which themselves have alicorn magic. Perhaps the barrier was also meant to trap Opaline, as her castle is obviously within the traditional Equestria of G4.
Opaline is an enigma. If she has been an alicorn since the beginning, it is possible that she came from “the alicorn civilization” that the royal sisters had written about in their diary. That could explain her opinions about the alicorns, and why she took Sunny’s humility as a strong provocation, she was not a “proper” alicorn. And if she had lived that long, it could mean that she came from the time when the magical caste system existed.
And since she could assimilate magic, although she could only do so with fire-based magic when she was so weakened, it’s possible that her kind is very special. None of the other G4 alicorns had demonstrated that they could steal other people’s magic, although Cozy Glow had taken stolen magic from Grogar’s bell to become an alicorn. She does not use Tirek’s technique of draining magic from living beings, which may have been developed by the centaurs to survive in magic-poor environments. Instead, the magic is assimilated into the body and consumed until it disappeared. Tirek cannot consume other people’s magic in his body beyond replenishing his mana reserves. Opaline consumes magic. Could it be because she is a fire alicorn?
If this is the case, it was no wonder that the Mane 6 had to steal the magic from Opaline who they didn’t want to kill because they don’t know what consequences it could lead to (Sombra always returns), chaining her to a castle for all eternity . Opaline’s status as an alicorn meant that they had to treat her somewhat more leniently, and they couldn’t send her to Tartarus because there is magic there. They were clear about how dangerous she was.
And it is possible that Opaline has several screws loose in her head due to immortality and the ability to consume other people’s magic. She was unbalanced in E8, which Misty was alarmed by.