Applied Starlight: Explained · 5:30pm Jun 25th, 2014
The left image was a thrown-together pic I sent to AquaGalaxy, depicting a scene from Chapter 7. The right image is what she sent back to me. I was very happy that day.
When I posted Chapter 20 of Applied Starlight, I said that at some point in the future I would write a blog post explaining my own interpretation of the story if no one figured it out. To my delight, it turns out I don't have to do that, because Monarch Dodora actually succeeded in my challenge. Click here to read the comment in question, and also be sure to read some of the comments following that.
While there are still some minor details that aren't covered by Monarch's explanation (specifically, the purpose of the first link—the YouTube video—has yet to be answered), the core concepts of the story have been, and that's the most important part. I've decided to leave those minor details unexplained in hopes that someone in the future notices them and figures them out (now that I have confidence in myself that I actually can write a solvable puzzle).
However, there is actually one huge thing that has no explanation, and was left completely up in the air. Other parts of the story can be puzzled out, but this one had no clues whatsoever. No form, no shape, no canonical existence. It's one of the biggest questions of the story, too:
What are the stars?
The nature of the stars was deliberately left ambiguous, and a lot of ideas have already arisen: it's the journal's narrator, it's the sun, it's Discord, it's Starshine, it's a corrupt spell, it's Twilight's alternate personality, it's some entity chilling in the cosmos, or—an amusing idea by Sealcake—the stars are the readers themselves.
So, what's the answer, you ask? Well, there is no answer! That's why I left it ambiguous! You can decide for yourself!
...
*dodges rotten tomato*
Okay, fine. I'll explain the idea I had in mind while I was writing the story.
I always personally considered the stars—or, more accurately, the entity that calls itself "the stars" (the stars are filthy liars, after all)—to be a form of Corrupted Harmony (if you've ever read You Can Fight Fate you should already know where I'm going with this). They are playful, arrogant entities that can exert influence over ponies' actions and thoughts, particularly those connected to the force of Harmony. Their goal is to bring Harmony to the world, but they completely misinterpret what that means—they think that that means that everyone should live in a world of forced happiness and no conflict.
Twilight has caused a lot of conflict in Equestria—look how many thousand year-old villains have come back, look at how the changeling invasion... look at just how much stuff happens to the peaceful land of Equestria now that Twilight's around. The stars blamed her, so they tried to kill her (in the most over-the-top way possible, by literally removing her from reality) but Twilight survived through sheer force of will. Thus, the stars went to Plan B: draw Twilight into the world of G3, a place of no conflict at all.
They failed at that too. The stars are Corrupted Harmony, but Twilight's talent and destiny is Harmony. In the end, she'll win every time. 
That's all. Hm. Is there anything more for me to say...?
Oh! Oh yeah! I just wanted to mention this: quite a lot of Chapter 5 (the white glass chapter) was one big homage to One Over Zero, even including smashing the glass with a rock to break it.
https://www.undefined.net/1/0/?strip=558
https://www.undefined.net/1/0/?strip=560
I highly recommend the series. Here's a link. Go read it.
As one final note, previously in the comments section for the story, I explained what Twilight originally did to Applejack and Sweet Apple Acres to make her go off the deep end (and start the story off in the first place). Read that here.
I'm pretty sure that's it. The two-week tale of Applied Starlight is over and done. It was fun. If you have any questions about anything—confusion about some event in the story, clarification for something or another, or even just questions to me about something—then feel free to ask! I'm happy to answer, and I'll answer frankly. No more twisted puzzles. 
Thank you for reading!
Is the above explanation not good enough for you? Continue on to "Applied Starlight: Thoroughly Explained".
...and NOW it all makes sense.
Did you write all that in only 2 weeks? That's extremely super very impressive. If it's cool, I'd like to talk more about writing with you on Skype. I'm bgchandler.
2247833 Nah. It's been in my head for a long time, but most of what you see was written throughout Season 4. I think I finished it the day of the finale, actually. It took a while to publish it because I was waiting for the cover art.
"Two week tale" implies the wrong thing. I meant that between the time of publishing the first chapters of the story on Fimfiction and posting this blog, about two weeks had passed, so from the reader's perspective it's been a self-contained two weeks.
I almost never use Skype, sorry.
Thanks for reading!
...well, time to read it over again. I *REALLY* want to know what that first link was all about...
2587835 In a few days (once I actually get around to it), I plan to write another blog post that'll explain absolutely everything—nothing ommitted or left ambiguous. It's partially in "celebration" of the story getting on EQD, but mostly because people keep on asking really good questions that haven't been answered. So... look forward to that?
2587850
Absolutely! I'll take that as an excuse to re-read the entire thing in a new light in that case! great job on everything!
2588495 Y'ello again. In case you didn't get it in your feed, the full, insane explanation has been posted.
Ha! I was totally reminded of 1/0 when I was reading some of those early parts. That it was intentional is awesome.
2815990 One Over Zero is awesome.
While I understand why a webcomic that ran from 2000-2003 isn't very well-known today, it really ought to be!
Minty ironically caused Conflict too with her OCD shattering the bacon candy cane for Santa.
And PRINCESS RARITY caused conflict because she was more interested in enjoying herself than preparing for the duty SHE WAS MADE PRINCESS FOR TO BEGIN WITH!
And Spike caused Conflict on a personal level with Wysteria, finding herself stuck in a role of princess she didn't truly want, and she made everyone princess rendering the rank meaningless (which was her intention).