What lies between shadow and light: Hints and solution

[mmammel]

Here I will post some hints to solving the puzzle and later a walkthrough.

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Here are hints for each part to give you a good idea of what to do:

Spoiler below!

1) The anagrammed text hints at Fibonacci sequence. Bloody_Eugene posted the unscrambled text: "These hole digging critters have a population that increase rapidly. There must be a way to track this development and make the infestation come to an end." (The Fibonacci sequence describes the increase in rabbit populations.) In the Fibonacci sequence, each term is the sum of the previous two terms. The standard sequence starts with the seeds 1,1 and goes 1,1,2,3,5,8,13,21,34……

2) For the transformations listed:
T -> B
C -> C
Q -> H

Villane observed
20 T -> B 2 ( 2+0 = 2 )
3 C -> C 3 ( 3=3 )
17 Q -> H 8 (1+7 = 8)
In other words, change a number to the sum of its digits. You could also view this as applying MOD 9 if that’s easier for Excel or yourself. But there is one slight difference. Now what do you do with this transformation? Do not apply it to the cipher text! Apply it to some numbers you will have.

3) Silently evil emerged darkness.
kenji.nanashi noticed the initial letters spell “SEED”. This means that the answers to the next two sequences are the seeds for a Fibonacci sequence.

4)
3, 9, 7, 4, 8, 9, 5, 7, 11, 6, 6, 13, 7,
8, 6, 9, 6, 11, 8, 13, 10, 15, 8, 11, 4, 9,

Bloody_Eugene posted a solve to the first sequence, break it up by every third number:
3,4,5,6,7..
9,8,7,6…
7,9,11,13…
So the next number in the sequence was identified as 5, which is the first Fibonacci seed. The next sequence may not have been solved completely. Spukrian and I posted possible reasons why the next number could be 6 but I’m not sure if they were valid. But by trial and error, I determined that 6 was indeed the second seed.

Now you have a key. Hint from Thomas: Less-safe-procedural-Vernam.
A Vernam cipher adds a random sequence key (for safe procedure) or a generated sequence (less safe) to text to be enciphered.