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Sorry for the size of the text, but it’s a big theory. Click it and it’ll zoom in :)
This fixes all of the issues with G5’s magic, makes G5’s backstory more tragic, makes the world more believable and honestly made the show so much more fun for me once I figured it out. Picturing a disembodied Twilight watching Zipp and Pipp singing, lighting up crystals to let them know help is on the way, or at the very least to help them find an exit… It made an already beautiful scene all the better.

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Background Pony #3788
It IS true that the rules for magic from G4 are far too different from the norms in G5, where magic sometimes seems far too easy and self-assured without magic users having to do anything. Everything indicates that the Unity Crystals have an intelligence of their own, and it is easy to see that magic has become self-aware in response to the ponies, especially the Mane 5 through their cutie marks. The cutie marks in the ponies had evolved, and become far more magical potentially, which is why Opaline is planning to steal them. Under normal circumstances the ponies should do as they were accustomed to with their instincts and training, but in many places little or no effort is seen from the ponies themselves. This is not really good since advanced magic becomes unobtainable when normal magic becomes too easy for ponies.
The link between the Unity Crystals and the Wishing Star may suggest that these crystals are a “gate” between the world and Twilight herself, who may have imprinted her own intelligence on them. The three crystals had “fallen from the sky” according to C3, and these must have been important to the ponies in the early days.
When Zipp and Pipp argued, we see that their magic began to have an effect on the surroundings. Just like in C1 and other TYT episodes. These crystals glow because they received pony magic, which had “leaked out” during the argument. This proved once again that the ponies have a serious problem with them “polluting” their surroundings with unwanted and powerful magic that can affect the natural conditions and animal life. The Unity Crystals were not only to protect magic from magic thieves like Opaline, it was also likely to prevent unwanted “pollution”.
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ThePonyTheorist
Non-Fungible Trixie -

@Jazepony
Interesting idea!
What stands out to me about Argyle is how his lighthouse is full of magical artifacts. perhaps he was studying ancient magic, and had an artifact nearby which Twilight could connect to, to briefly strengthen her power?
Or it could be that her mind is specifically trapped inside the earth pony crystal, and the other crystals were inert.
I mean, just from the top of my head, I remember that he had Grogar’s bell (which could be used as a reservoir for Twilight to access if she came into contact with it) - and he was even investigating the memory stone, which I suspect could be used to communicate with Twilight if he ever managed to find it…
It’s definitely a fun idea!
deactivated8e8d7c

I really absolutely love this theory ! It explains a lot about G5 ! It might even explain Argyle! Maybe Argyle used to be no different to than the other earth ponies of Maretime Bay before pony unity! He might have just randomly found the Earth Pony crystal out of nowhere and Twilight at the moment he touches the crystal out of curiosity begans mind controlling him making him the way he became and then passing it down to Sunny and thus, the rest is history. But now it raises the question of why she didn’t do the same to Alphabittle or Queen Haven when they owned the crystal for so long too !?
ThePonyTheorist
Non-Fungible Trixie -

@Background Pony #5E1A
OOC explanations basically break the whole point of canon
Even if she’s in her small form due to using up so much of her magic, it doesn’t explain her bizarre choice to gate the warning about Opaline behind earth pony magic, and the way magic has just completely broken vs what we knew of the G4 canon. Magic has rules, G5 breaks most of them. A 3rd party casting all the magic we see solves it.
Background Pony #5E1A
Twilight is dead. Gone. She isn’t coming back. Hasbro would never bring her back. Her being in her small alicorn form in the hologram can be explained simply by the fact that it is too hard and expensive to animate her mane in her Twilight 2.0 form. But even then they can say that she used all of her magic to protect Equestria’s magic and that’s why she is in her small form. Did people forget that Luna also had a small form when she was weak?