Amazing chapter, just amazing! The Spaceys are in for it now.

Dear Princess Twilight Sparkle, when you help your Friends release their Evil Mothers, they might become part of the same Space Zoo as you and your Brother are in, so good luck.

Now for chapter 2.

"What about Celestia, or Luna? I mean if they could move the sun or the moon, maybe they could move it, or block it with the moon. Can't Discord just... snap it out of existence?"

But why wouldn't blocking the asteroid with the moon work? Twilight didn't actually answer that. Even if the moon and asteroid end up completely shattering each other and cause millions of smaller meteorites to rain down on the planet, that would still be preferable to a giant asteroid. Since this is a literal extinction level catastrophe I'm surprised they didn't try it.

In fact, the asteroid might not even need to hit the moon. Just getting them close enough to create a gravitational slingshot might be enough to make the asteroid miss the planet.

The door in the back opened and several of the bipedal creatures entered the room with poles and rope to wrangle the cragadiles, pulling them away from the guarded nest while another handler swooped in and collected the eggs from the nest.

Well that gives some rather unpleasant implications for the other's trapped in this spaceship

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Maybe she can only control where the moon is within its track, and this asteroid is coming from out of plane.

They could open the portal to Canterlot High School Earth and evacuate as many creatures as they can while there's time.
But the main characters would feel bad about leaving while others stayed behind.

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Even so I think they could force it off to sacrifice it. Its a lot easier to break something then to build it. Also if that's the case then there's more mystery of who built it but I guess it's a pretty classic headcannon that Equis was hoof built. Also when twilight rose the sun it was all wobbly over the sky

Though his own transformation had made him taller, she would always seem larger than life to him. Even if he shapeshifted into a massive bugbear, she always made him feel like he was an inch tall.

She knows that. And she's very proud of it.

"Sorry, sorry about him!" Thorax apologized. "He's just being a grumpy grub. Pharynx, this is why I can't take you anywhere, you're embarrassing us!"

Who of them is the older one again?

They both screamed at each other, "What did you do!"

Of course they would instantly blame each other...
(Also, I suggest replacing the "!" with "?!"to make it sound like an angry question.)

She looked around the room. There was nothing. The room was a box with four walls, one of them being a transparent floor-to-ceiling window.

They could have at least added a bit furniture.

"Even if Equestria hasn't been destroyed, we're too far away. We have no magic. We can't shift. So... what's plan B?" he asked.
She stared at him.
He stared at her.
"... Fuck!"

Aliens: "We approve this plan. In fact, we greatly encourage it."

Chrysalis looked at the spreader bar on her ankles, and then at Thorax.
"I know how we get out of here."

Go on...