Magic, Friendship and the Elements of Harmony · 7:25pm Feb 2nd, 2015
Many months ago I made a post about how the season 4 finale makes sense. Linky here. The gist of it is that there are two kinds of magic. magic (lowercase m) that is standard unicorns casting spells, pegasus moving flight, etc; and Magic (capital M) that is the Magic of Friendship; or if you will Friendship is Magic. The idea was that Tirek was able to steal the Main 6's magic, but not their Magic. However I got stuck on trying to explain how they were able to use their Magic and how it tied into the box.
What I realized was that the origins of their rainbow power abilities begins with their ties to the Elements of Harmony. Back is season 2 we saw what happens when the Main 6 (Main 5 plus Spike really) try to use the Elements while not friends. Because of Discord's tricks the 6 were not friends, and thus had no Magic to power the Elements with. Once they were reunited however, they worked fine. Likewise, in the season 3 finale the blast that came from the Elements that changed Twilight was the reuniting of the friends and all the rest of that stuff. Twilight's completion of Starswirl's spell unexpectedly activated the Magic.
What this tells me is that it is the Elements of Harmony that give our heroes the ability to harness Magic. But come season 4 they have to return them to the Tree of Harmony. This would have left them without the ability to use Magic. But then came the box. Just as the Elements were a part of the Tree which let the main 6 use Magic, so too was the box. But unlike the Elements, this power is inside of them, without the need of any artifacts.
My greatest evidence for this idea comes from Rainbow Rocks. Where 5 high school girls can suddenly use magic without the need of any artifacts. My assumption is that when the box was opened, the gift of Magic use was given to the main 6, but as they defeated Tirek and returned the magic all across Equestria the Rainbow Power, the ability to use Magic also spread through Sunset Shimmer's journal into the human world. There it latched on to the people who harnessed Magic in the past; Rainbow Dash, Fluttershy, Pinkie Pie, Rarity, Applejack AND Sunset Shimmer. As Sunset said in RR "The magic of friendship can be turned into something horrible." She knows this because this is how she powered the crown in EQG, with Magic. And their new use of Magic is truly Rainbow Power because of all their new highlights, same as the ponies.
The Humane 6 must have discovered their new powers playing music together as friends. And the fact that Rainbow Dash on multiple occasions starts using Magic independent of the others is what truly tells me that this power is now within each one of them, instead of in the elements.