Page break. The guards in the Pinkie balloons have them surrounded, and T-1000 the Wonder Dog is guarding the door behind them, so it would appear they are trapped. Instead of just gunning them down like they easily could, the guards appear to be simply holding them down until Red Eye gets there, because he seems hell-bent on doing everything according to the Cliche Villain's Handbook.
Then, suddenly, Velvet Remedy's pet balefire phoenix, Pyrelight, shows up out of nowhere. It is all huge now, because it has apparently been bathing in the same radioactive crater as the mutant alicorn. It blows up all of the balloons, but unfortunately also blows up the balloon they had hoped to escape in. The scene ends with the two of them still marooned on the roof. How utterly pointless.
Page break. We rejoin our intrepid heroes at an indeterminate point in the future. They have presumably been captured, and are under guard in some kind of weird room filled with red steam. Probably one of Red Eye's toxic fart caverns or something. We are told that their capture was as "ignominious as it was inevitable." There are a pair of griffon guards and the robotic dog watching them. Suddenly, Red Eye himself enters the room.
>“Littlepip,” he said graciously. “Sit, relax. I mean you no harm.”
>Obviously, the same couldn’t be said for us. I was still processing the mere notion that Red Eye would lock himself in a room with us when Xenith charged at him, murder in her eyes.
Obviously, Red Eye's statement was intended explicitly for the two of them, so this remark of Littlepoop's makes no sense. What the author appears to be trying to say is that Red Eye asked Littlepoop and Xenith to sit and relax, but Xenith does the exact opposite of that and attacks him instead. However, in a misguided attempt at wit, he chose a particularly awkward wording. My best advice for kkat here is that he should get a better grasp on how to use language before attempting to be clever with it, particularly if he wants to get away with tossing words like "ignominious" around.
Anyway, Xenith's attack naturally backfires, because Red Eye has them in some kind of magical force field or something. Littlepoop figures out that this is the significance of the red mist: it is hiding an alicorn shield. Why Red Eye would need to hide such a shield from them, or why he would use red mist to do it, or how Littlepoop was able to ascertain all of this from the information she has available...are all questions for another day.
>Red Eye beamed at me. (Literally -- in the mist, the line of red light shooting from his cybernetic eye was clearly visible.)
This pun demeans us all.
ANYWAY, it turns out that the reason Red Eye hasn't killed them yet is that he wants Littlepoop to do something for him:
>“All I want you to do is something you were going to do anyway,” Red Eye said in a tone both casual and infuriatingly confident. “I just want you to do it on my timescale.”
>“I want you to kill the Goddess.”
I mean...yeah, when you think about it, I guess it makes sense that Littlepoop was going to kill the Goddess eventually. I mean, sure, we haven't heard anything about an actual Goddess even existing, and so far Littlepoop hasn't said anything about wanting to kill her. However, Littlepoop's only goal in this story seems to be to run around randomly killing whatever giant evil things she happens to encounter, so I guess it stands to reason that she would get around to killing the Goddess eventually, assuming such a creature existed.
>Okay, I did not see that coming. “B… but you serve the Goddess! You… you’re Her high-fucking-priest!”
Is he? I don't think that was ever clearly established. All we know about this guy is that he believes he has been hearing messages from a Goddess, who supposedly ordered him to do all the crazy shit he's been doing. Again, we don't even know that there actually is a Goddess at this point. Just a short time ago it was established that both Celestia and Luna perished when some kind of pink cloud descended on Canterlot, and as far as I'm aware the two of them are the only ponies in this story who could qualify for godhead.
Anyway, Red Eye goes on to explain that he and the "Goddess" are partners, but that they no longer see eye to eye on things, and he's chosen to break their partnership in the manner usually chosen by cartoon villains. He was impressed by Littlepoop's handling of the gigacorn a few scenes ago and wants to give her the task of killing whichever not-really-dead Princess the "Goddess" turns out to be. At present, my money is on it turning out to be Luna, who went mad during the war and reverted back to her Nightmare Moon persona. But, I suppose we shall have to wait and see.
>“As I’m sure you’ve noticed, the Goddess controls Her children. Telepathically. They are not so much individuals as they are extensions of Her will. And they will remain so until She is finally put to rest.”
None of this has been established. Like a lot of this author's ideas, this one isn't necessarily bad, but his execution is terrible. Something like this needs to be built up to in small degrees; by the time it's finally revealed, the reader should have mostly figured it out from the breadcrumbs that have been dropped. As I said, we don't even know that this Goddess even exists as an actual character; up until now, it's been sounding as if Red Eye is the final boss and the princesses are both dead.
Anyway, blah blah blah. Red Eye keeps yammering for awhile, and the gist of it is that he plans to kill the Goddess, and then once the alicorn hivemind is dead, he will join the "Unity" himself and become the new Celestia, assuming the tasks of raising the sun and moon and manipulating the weather. Even sillier still is that he intends for Littlepoop to take his place as head of...whatever the hell he's currently the head of. "Red Eye's Emporium of Slavery and Generic Bad Guy Stuff" I suppose.