Muffins at the End of the Universe, a writer's companion, volume three

Part of the challenge I gave myself with Muffins at the End of the Universe was writing an a confined environment. When your resources are limited it can sometimes lead to the best ideas, so for the first two stories I limited myself to working within the interior of the crashed pod, the Doctor's laboratory being a prime source of plot material. Rules are there to be broken however, and so Year Zero sees Twilight, Trixie, Derpy and Doctor Whooves venture outside the pod for the first time. Of course the whole joke is there is actually very little to explore in the barren wasteland beyond the pod so it does not open up as many new possibilities you might first imagine.

Notably the "alien" crate that drives much of the second chapter can ultimately be traced back to the pod, even though it was found outside. Indeed there is an undercurrent in the story, I feel, that the main characters are gradually being driven mad by boredom, creating their own wacky diversions for themselves, like aliens and phantom phoenixes, in the absence of anything else to do. But they are merely like hallucinations; wild imaginings.

Tracing the characters' motivations, it made sense to me that Twilight and Trixie would play a trick on the Doctor to get back at him for scaring them with his prank. Doctor Whooves meanwhile is motivated by his desire to convince those around him not to believe in superstition, but to embrace science instead, and he will go to great lengths, as in Year Zero, to try and accomplish that end. While his own belief in aliens is equally, if not more absurd, especially in the universe of Equestria, it is characteristic of his science-oriented eccentricity. It further indicates that he is an ordinary (I use that term extremely loosely) earth pony as opposed to a time-traveling alien himself, as in other portrayals.