By Ben Monreal

This is a multi-step puzzle. Step one is to solve all the clues associated with the defendants; each answer has a standard military rank abbreviation hidden in it. Each such rank is (uniquely) associated with a pay-grade, from E1–E11 or O1–O11 for enlistees and officers. (While some rank abbreviations are used for different pay grades in different services branch, each defendant's branch is given here.) Sort the characters alphabetically and use the pay grade number to index into the character's name.

BranchClueAnswer/RankPay gradeDefendant
USAF English beer cocktail shandygaff O11 Blaise Barrier
USN Smelly compounds added to natural gas mercaptans O6 Camryn Cheddar
USN Mass divided by volume density O1 Deng Dragoon
USAF AKA German turnip kohlrabi E1 Erin Erg
USA Non-SI unit of radiation exposure roentgen O10 Fatimah Fox
USN State formerly in Yugoslavia Bosnia and Herzegovina E3 Gabby Gadfly
USN Element 48 cadmium O10 Hermione Hyrax
USAF It can be retrograde or anterograde amnesia E2 Ifeoma Ifill
USA Coating via galvanization zinc plating E4 Jerry Jetski
USA Honey Boo Boo matriarch Mama June O4 Katashi Kneecap
USN Package management system for OSX MacPorts E7 Lew Liftgate
USN Protagonist of The Crow Eric Draven O5 McGregor Muggle
USA Catshill’s district Bromsgrove E8 Norah Normalville
USA Thermoplastic adhesive sold in stick form hot melt glue O9 Olivia Omnibus
USA High-pitched woodwind piccolo O6 Pip Primordial
USA One of four fundamental states of matter plasma E9 Quint Quizbowl
USN Lightweight craft wood balsa E2 Rebecca Rotifer
USAF Philosphical principle of parsimony Occam's razor E4 Spiros Spokane

You should extract INDEX BY FRATERNIZER.

Next, get to work on the next set of clues. Note that the cited UCMJ article prohibits fraternization between officers and enlistees. The ten pieces of evidence serve to “pair up” the characters. “Captive bolt gun” contains the substrings “capt” and “ltg,” which means that the captain (Camryn Cheddar, pay grade O6) fraternized with the lieutenant-general (Olivia Omnibus, pay grade O9). (Some of the pairings are between two enlisted ranks, or two officer ranks, rather than enlistee-officer, which is why some of the defendants are pleading guilty and some are not.)

Three-word stop on outer half of Craigieburn Line Broadmeadows Railway Station
Anton Chigurh’s weapon of choice captive bolt gun
Collective term for large animals whose conservation is especially popular charismatic megafauna
Common animal protein collagen
A specialist like Dr. Douglas Filmore from Bones forensic podiatrist
The royal we, formally majestic plural
Nickname of Seattle’s first madam Mother Damnable
Mr. Mxyzptlk’s girlfriend Ms. Gsptlsnz
One of the three varieties of Athenian theater satyric drama

So, repeat the extraction from the introduction, but using the character's partner's pay grade rather than the character's own.

NameRankFraternized withPay gradeNth letter of name
Blaise Barrier gaf sma E9 r
Camryn Cheddar capt ltg O9 e
Deng Dragoon ens cpo E7 a
Erin Erg ab amn E2 r
Fatimah Fox gen col O6 a
Gabby Gadfly sn msg E8 d
Hermione Hyrax adm sra E4 m
Ifeoma Ifill amn ab E1 i
Jerry Jetski cpl maj O4 r
Katashi Kneecap maj cpl E4 a
Lew Liftgate cpo ens O1 l
McGregor Muggle cdr sa E2 c
Norah Normalville msg sn E3 r
Olivia Omnibus ltg capt O6 a
Pip Primordial col gen O10 d
Quint Quizbowl sma gaf O11 o
Rebecca Rotifer sa cdr O5 c
Spiros Spokane sra adm O10 k

REAR ADMIRAL CRADOCK was, in answer to judge's inquiry, Sir Christopher “Kit” George Francis Maurice Cradock KCVO CB SGM, who went down with his ship when it sank at the Battle of Coronel during World War I. The answer the judge is looking for is that ship, the HMS . . . what? GOOD HOPE.