Something’s Brewing by Poat

Puzzle explanation

In column order, answers with letters omitted were: 20 school(b)ag, 2 th(a)wy, 3 ar(b)or vitae, 24 archa(i)sm, 18 ill see(n), 5 (g)olfers, 14 hear(t-t)o-hear(t), 6 cast(o)r, 16 Lyse(n)ko, 30 cheru(p), 19 minke wha(l)e, 8 dumf(o)unds, 31 ear(t)hs. The omitted letters spelt out “Babington plot”, an Elizabethan conspiracy in which encoded messages hidden in the stopper of a beer barrel were exchanged with the incarcerated Mary Queen of Scots. Thematic answers (10 message, 13 letter, 25 epistle, 27 note, 37 missive, 38 dispatch, shown in italics in the table below) were encoded using a substitution cipher with the keyword BUNGHOLE. The original correspondence, intercepted by a double agent, provided sufficient evidence to convict Mary of treason.

The keyword string is shown below the alphabet as follows:
ABCDEFGHIJKLMNOPQRSTUVWXYZ
BUNGHOLEACDFIJKMPQRSTVWXYZ
Thus the M of MESSAGE is encrypted as I, etc.

Clue explanations

Conventions: * = anagram, < = reversal

No Answer Explanation
Across
1 STAGY STAG PARTY − PART
5 ORCHARDS (MAYORS − MAY) about CHARD
10 MESSAGE MASSAGE, E(xaminees) for A
11 ASTRUT ASTRONAUT − (ON + A)
12 TWOER TWOCCER − CC
13 LETTER (s)ETTER after (tria)L
15 BEETLE OFF Homophone (BEATLE) + OFF; reference RAF slang, kite = plane
17 DEVOIR RIVED < about O
20 STIR GRITS < − G; reference terms for prison
22 ROSSINI Hidden; reference opera William Tell
23 AT A LOOSE END ALOO in EAST END *; pie = confusion
25 EPISTLE SPLIT * in EE
27 NOTE CENOTE − CE
29 EOCENE EO + homophone (SEEN)
32 ON THE BALL Alternate letters + LABEL *
34 CAVORT AV in CORTEX − EX
35 LEHAR H in LEAR; reference Merry Widow
36 AUSSIE ISSUE * after A
37 MISSIVE VIS < in MISE
38 DISPATCH PATCH after DIS; reference Detective Inspectors
39 QUEYS Q + UEYS
Down
1 SITED I in STED
2 THAWY WHAT * + (barle)Y
3 ARBOR VITAE A + (BOAT + RIVER) *
4 GREBO OGRE − O [with] BO
5 GOLFERS (L + F) in GORSE *; Carnoustie is one location of the British Open Championship
6 CASTOR Two definitions
7 ATHEISE ATHETISE − ’T; reference The God Delusion
8 DUMFOUNDS F(inger) in (DU + MOUNDS)
9 STIFFISH TIFF in (S + SH)
14 HEART-TO-HEART THAT, TO HEARER *
16 LYSENKO Composite anagram of MILTON KEYNES using (MET + IN)
18 ILL SEEN NELLIES *
19 MINKE WHALE MINK + WE < + HALE
20 SCHOOLBAG (HOLS + GO + ABC) * & lit
21 TAMANDUA U in DA after (TA + MAN)
24 ARCHAISM (p)HARMACIS(t) *
26 PELTAE PELT + AE
28 OBOES O in OBES; reference organ stops
30 CHERUP CHERU(b) + P
31 EARTHS HEARTS, H inside
33 WAVY Two definitions
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