This is a really nice puzzle! To break into it...
So we know where the plane was leaving from - where was it travelling to? Without any coordinates to find this out (all the numbers are obscured by the coffee spill), we need to:
The logic that I followed to solve this was roughly as follows:
Finally, we can identify the 3 characters in the destination ...
There are two steps you need to follow to decrypt your message:
It soon becomes clear why you have chosen this combination of numbers in your encryption process, as the plaintext contains:
The fully deciphered message (a few corrected typos indicated in square brackets) reads:
While points concerning the plot of a story tend to be the domain of Literature.SE, our business on Puzzling.SE is puzzles - and this is a question about a puzzle. Namely: I think I have decrypted a cipher (albeit a particular one from a specific short story) - how can I make sense of its output? Here's an explanation for the OP, along with some general ...
Heavy credits to the other two answers.
Everyone keeps saying the answer is
However, I disagree because:
Hence, the answer is:
Yes, I know that this is ridiculous, but this bounty being there is honestly super annoying, so i'm posting this so it goes away.
A couple of the "words" are easy to recognise as actual words:
so I suspect that
It's now clear that the message is
so the ordinals are
and the system is
This is also consistent with the hint.