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Chroma's plot - Actual spoilers!
Previous ChapterNext ChapterAlright. Chroma is more than just a way to use a ME3 ending.
Okay, no, it's not. Still, more thought went into it than I could portray.
What was going on in the first ending? It's implied that the Queen had planned for it all to happen as it did. The question is where Midnight came from. Most likely, it actually is her shade, given that Twilight is NOT connected to the hive mind and the Queen never really bothered with Midnight. She also directly opposes the Queen and her interests. Other than Mirage whom she considers almost a daughter due to her Changeling side, Midnight just never had anything that'd interest her. Also, she 'died' soon after being connected to the mind.
So what about Few? First off, neither of those chapters was actually supposed to be in the story, but they were handy for when I just wanted to write. Like Few, which I wrote at 2 AM. You're welcome.
While there are no definite answers, it's strongly implied that Mirage has been controlled - indoctrinated, if you will - by the Queen. But how could that work? Well, We've learned that she secretly rebred Changelings and rebuilt the actual hive mind. But only actual Changelings (or Shapies, anyhow) were connected to that due to its nature. Thus, the Queen could plot without Daylight finding out, but she couldn't directly control her either. But if she wanted any hopes of doing a quick takeover, she'd need control over all, not only Changelings. Thus, she had to bait Daylight into recasting the spell and controlling the hive mind, but simulatenously becoming a part of it.
As such, the Queen could then take back over and rule everyone. But what about Twilight's apparition? An illusion brought into Daylight's mind using the weak link that she did have to the Queen. Doesn't she seem quite out of character? No motherly love, not even any recognition. That's because all the Queen had to work with were Daylight's memories of her. Also, how would Twilight notice Daylight calling out to Mirage, which the Queen enforced to be not answered?
After slaying her wife and daughter, Mirage joined the offensive on the ponies semi-voluntarily. As one of those who ushered in the new age however, she became a hero for both sides by slaying the Queen. Or maybe she didn't. I'll leave that up to you. After that, she recorded the time capsule, which unfortunately had to be used as intended.
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