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(This is part of a series of puzzles written for Timwi for a Secret Santa puzzle exchange, themed around various custom modules for the game Keep Talking and Nobody Explodes. No KTaNE knowledge is necessary for any of these puzzles except the final meta; each puzzle resolves to a single word or short phrase.)


On The Subject of Dr. Doctor

A good doctor always sticks to a strict code.

enter image description here

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@Stiv has figured out the initial step, the next steps are to

Apply the transformations applied to the coded message onto its answer.

Message 1

Change colours of first 2 maritime flags of each word.
Answer: LUNE
Transformed: ULNE

Message 2

Squish braille letter so that 3rd row becomes 2nd row.
Answer: URANIUM
Transformed: HRANIUM

Message 3

After the first letter, add a copy of the first letter but with any open sides "flipped" to the opposite side, and with the dot reversed. Before the last letter, add a copy of the last letter rotated 90 degrees clockwise. (Thanks @hdsdv)
Answer: ROIS
Transformed: RAOIUS

Message 4

No clue, but the 2 incorrect letters are symmetrical in semaphore.
Answer: FOUR
Transformed: FSMUR (backsolved)

Message 5

Reverse the morse code of last letter in each word.
Answer: TITIN
Transformed: TITIA

Final Extraction:

These are all 1 letter away from the name of a bone:
ULNE -> ULNA
HRANIUM -> CRANIUM
RAOIUS -> RADIUS
FSMUR -> FEMUR
TITIA -> TIBIA

Answer:

The changed letters in the bone names are ABCDE, giving an ordering for the one-off bone names. Reordering gives the answer ETHOS.

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    $\begingroup$ For 3, it is rot13(nsgre gur svefg yrggre, nqq n pbcl bs gur svefg yrggre ohg jvgu nal bcra fvqrf "syvccrq" gb gur bccbfvgr fvqr, naq jvgu gur qbg erirefrq. Orsber gur ynfg yrggre, nqq n pbcl bs gur ynfg yrggre ebgngrq 90 qrterrf pybpxjvfr) $\endgroup$ – hdsdv Feb 9 at 2:07
  • $\begingroup$ Thanks, I'll add it to the answer. $\endgroup$ – Zimonze Feb 9 at 2:08
  • $\begingroup$ For 4, I think this may be it. There aren't really enough examples to verify one part, but that part isn't relevant to the answer. rot13(Pbafvqre whfg gur erq gevnatyr ba rnpu synt. Vs vgf evtug natyr cbvagf va n pneqvany qverpgvba, ebgngr vg - nagvpybpxjvfr sbe gur yrsg synt, pybpxjvfr sbe gur evtug synt. Vs gur evtug natyr cbvagf gb n pbeare, whfg pbcl gur synt nf vf. Guvf tvirf gur svefg vapbeerpg yrggre. Sbe gur frpbaq, nf lbh abgrq, whfg syvc ubevmbagnyyl.) $\endgroup$ – hdsdv Feb 9 at 2:18
  • $\begingroup$ @hdsdv I don't think that's it. It seems way more complex than the others, and the "flags" in the puzzle don't even have the red/yellow triangles. $\endgroup$ – Zimonze Feb 9 at 2:23
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    $\begingroup$ Think you've cracked the bits I couldn't at midnight last night! Well done +1 :) $\endgroup$ – Stiv Feb 9 at 7:56
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Partial answer - core of the puzzle uncovered but step to final answer missing... (see @Zimonze's answer for that)

There are 5 messages encoded in the image, respectively in:

International Maritime Signal Flags, Braille, Pigpen cipher, Semaphore, and Morse code.

However:

Each message has several seemingly deliberate mistakes within it...

Message 1:

Several of the flags (marked below in round brackets) have red where yellow should be, or vice versa, while others {curly brackets} have black where white should be, or vice versa. If we fix these, then we produce the message:
(D)(E)BUSSYS{C}{(L)}AIRE(D)(E)(B){(L)}ANK

Note that with added spaces this message spells out "DEBUSSY'S CLAIRE DE BLANK", the answer to which is LUNE (completing the title of one his well known pieces of music). Note also that all of the corrupted flags occupy the first two letters of each word in the message.

Message 2:

Three Braille letters here are corrupted, but the overall message appears that it should spell out "(E)LEMENT (N)INETY (T)WO", the answer to which is URANIUM after consulting the Periodic Table. Note also that the corrupted letters occupy the first letter position in each word in the message.

Message 3:

This Pigpen cipher contains several completely superfluous letters:
F(M)RENC(D)H W(V)OR(B)D F(M)O(P)R K(H)ING(U)S

This appears to give us the message "FRENCH WORD FOR KINGS", the answer to which is ROIS. Note also that the superfluous letters have been inserted at the second and second-to-last letter positions in each word.

Message 4:

The semaphore message also contains several mistakes, coming out as:
N{NN}MBER AF(B)TER T{QY}REE

Here it appears we should substitute a 'U' for the first NN, remove the B, and sub in an H for the QY to read the message "NUMBER AFTER THREE", the answer to which is FOUR. It appears that the second letter in each word of the message is replaced by 2 others (if you consider an F to FB replacement in the second word).

Message 5:

The Morse code translates to:
PROTEI(A) HAVIN(W) (N) FAMOUSL(Q) LON(W) NAME

This appears like it should read (with substitutions) as "PROTEIN HAVING A FAMOUSLY LONG NAME", the answer to which is TITIN (see this link, for example). Note that in each of these cases the last letter of each word has had its Morse configuration reversed, even the last one where the reverse of E (a single dot) is itself!

Altogether then we appear to have:

LUNE, URANIUM, ROIS, FOUR, TITIN

At this point I had to go to bed, and had not quite pinpointed the patterns to the corrupted letters (thanks to @Jens and @athin for their comments overnight) and so did not appreciate how to define their derivation and figure what was required next. In the meantime the remainder of the puzzle was solved by @Zimonze - so now go read their answer after this one to finish the story!

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    $\begingroup$ A few observations: In message 1 the "U" is like the other oddballs, i.e. if you interchange yellow and red as well as black and white, it becomes an "L". In message 5, the substitutions are the Morse code reversed, i.e. "A" reversed is "N", "W" reversed is "G", etc. $\endgroup$ – Jens Feb 9 at 0:10
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    $\begingroup$ There are patterns in the errors, i.e. rot13(Zrffntr 1 vf svefg gjb yrggref, 2 vf svefg yrggre, 3 vf frpbaq svefg naq frpbaq ynfg yrggref, 4 znl or frpbaq yrggre, 5 vf ynfg yrggre.) So maybe they are for how to extract the specific letters -- maybe from those 5 words -- but it doesn't show any atm. $\endgroup$ – athin Feb 9 at 0:16
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    $\begingroup$ I just read Jens' comment, so maybe we will change the 5 words with the "error", e.g. the 5th word we should reverse the morse of the last letter. $\endgroup$ – athin Feb 9 at 0:22
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    $\begingroup$ Additional observations: In message 2 the first "E" is also corrupted. In message 5, the last "E" could also be "corrupted" as the reverse of "E" (in Morse) is also "E". As @athin points out, there is now a pattern to where the errors are located in each message. The only exception is message 4, where there is only one superfluous letter in the second word, instead of two.. $\endgroup$ – Jens Feb 9 at 1:22
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    $\begingroup$ One more observation: In message 3, there is a pattern to the superfluous letters. The first superfluous letter in each word can be achieved by mirroring the pigpen position of the first letter of that word and adding/removing a dot. Thus, in the first word, the "F" transforms to "M". The last superfluous letter in each word can be achieved by rotating the pigpen position of the last letter of that word clockwise by 90 degrees. Thus, in the first word, "H" becomes "D". $\endgroup$ – Jens Feb 9 at 1:56

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