Zones by Ten-Four

Gregson thoroughly enjoyed this puzzle by Ten-Four exploiting an unusual and serendipitous feature of the distribution of the vowels in the alphabet. The two letters unused in the answers are J and Q. The remaining 24 letters are paired in their natural order and the pairs then combined in their natural order to form six quartets. Each of these six quartets contains one vowel (counting Y as a vowel). Thus only the letters ACEHILORTUWY appear in zone two and only AEIOUY appear in zone three. The title of the puzzle is probably a hint to this zoning of the alphabet as well a reference to the zones of the grid.

Gregson's initial progress in zone one was swift. Progress in zone two was much slower until the pattern of coding pairs became apparent. However, even with knowledge of the coding scheme, the bottom right corner encompassing zone three was very hard to polish off with all the ambiguity in checked letters.

Congratulations to Ten-Four on what Gregson believes is a Listener debut.

ZONE ONE
1 Assassin's elite troops infiltrating college (7)
CASSIUS (CAIUS (college) round SS (elite troops))
6 To receive copy, women sit down (8, three words)
TAKE A PEW (TAKE (to receive) + APE (copy) + W (women))
12 Drupe alone developed base containers for seeds (11)
ENDOPLEURAE (anag of DRUPE ALONE + E (base - of logarithms)) Wordplay clearly indicates -ae (not -as), which is in turn easily justifiable in Chambers
13 No one's fashionable from the days of the Ark (7)
NOACHIC (NO + A (one) + CHIC (fashionable))
15 Coarse grass, hempen matting that's hard (4)
TATH (TAT (hempen matting) + H (hard))
16 Red books eaten by bear (7)
CARROTY (CARRY (bear) round OT (books))
21 Bridge partnerships: East leads, Ed's to follow (5)
ENSEW (E (East) + NS + EW (bridge partnerships - north/south + east/west))
27 Thorium's absorbing a mass of soft matter, a type of cotton (6)
T-CLOTH (TH (thorium) round CLOT (a mass of soft matter))
34 Missing from nursery, note, a set of six (6)
SENARY (SEMINARY (nursery) minus MI (note))
38 Academician enters chaotic tea-room; one that's required for co-ordination? (9, two words)
MOTOR AREA (anag of TEAROOM round RA (academician))
44 Edward's returning ethyl to make insect repellent (4)
DEET (ED (Edward) rev + ET (ethyl))
49 Warriors conceal wimpishness? Quite the opposite! (4)
IMPI (hidden)
52 Ferns and tea plants seen amongst irregular ceca? Aye (11)
CYATHEACEAE (anag of CECA AYE round THEA (tea plants))
53 Social worker's housing to distribute for the voter (8)
BALLOTEE (BEE (social worker) round ALLOT (distribute))
1 Measures of wit current society missed from the best in funny sitcoms (11)
CONCETTISMS (anag of SITCOMS round NICEST minus I (current) and S (society))
2 Immediately docking tail on a wild ox (4)
ANOA (ANON (immediately) minus last letter + A)
3 Expert's about to break down slightly (8)
SPARSELY (SLY (expert) round PARSE (break down))
4 One hiding note in storage unit (8)
SECRETOR (SECTOR (storage unit) round RE (note))
5 One gets taken in by criminal tuner and joiner (6)
UNITER (anag of TUNER round I (one))
6 Half a bar passed through a loop on a garment (4)
TOGA (half of TOGGLE (bar passed through a loop) + A)
7 Gibbon, perhaps, holds struggling petrel in a large plant (9, two words)
APPLE TREE (APE (gibbon perhaps) round anag of PETREL)
8 Stranger changes direction, becoming more slippery (6)
EELIER (EERIER (stranger) with R (right) replaced by L (left))
9 Letter by car is prompt (7)
AUTOCUE (AUTO (car) + CUE (letter))
10 Musical instrument is overturned on high-class sailing-boat (5)
PRAHU (HARP (musical instrument) rev + U (high-class))
11 Upset leaderless capital city (3)
EAT (SEAT (capital city) minus first letter)
14 Crude gumshoe appearing in oriental drama (6)
NO-TECH (NOH (oriental drama) round TEC (gumshoe))
22 One clue left to be composed, it's needed to progress? (8)
NUCLEOLE (anag of ONE CLUE L (left))
41 Plane crashed in Asian country (5)
NEPAL (anag of PLANE)
50 Molluscs and bird with no name (3)
MYA (MYNA (bird) minus N (name))

ZONE TWO
18 In a state of hurry, omit every other piece of farmwork (4)
AMOK (alternate letters of FARMWORK)
19 Curve's point furthest from the Earth, apparently missing (4)
OGEE (APOGEE (point furthest from the earth) minus AP (apparently))
23 Torrents of anger for Celtic when bad shots lose the league (5)
FUFFS (FLUFFS (bad shots) minus L (league))
26 Step in rennet I've misplaced (9)
INTERVENE (anag of RENNET IVE)
29 Merge by proxy with eastern town (6)
DIEPPE (DIE (merge) + PP (by proxy) + E (eastern))
30 Exercise? Forelegs injured, run cancelled (7)
SOLFEGE (anag of FORELEGS minus R (run))
42 Money's dubious, it's liable to fade (5)
MIFFY (M (money) + IFFY (dubious))
45 Good old granddaughter losing her heart? (4)
NICE (NIECE (old granddaughter) minus middle letter)
17 2, say, beside American river once (4)
OXUS (OX (anoa, say) + US (American))
20 Epic poem poet returned - Old English isn't acceptable initially (8)
EPOPOEIA (POPE (poet) rev + OE (Old English) + IA (first letters of isn't acceptable))
24 Letter about extremists, an enemy that's rejected surrender (7)
ENFEOFF (EF (letter) round NF (extremists) + FOE (enemy) rev)
25 Watch what Polyphemus failed to do, getting drunk? (11, four words)
KEEP AN EYE ON (KEEP AN EYE (what Polyphemus failed to do) + ON (drunk) semi &lit) Polyphemus was one of the Cyclops, blinded by Odysseus whilst drunk
28 Red seaweeds warping, aired in ice (9)
FLORIDEAE (FLOE (ice) round anag of AIRED)
31 Copy Australia, a cover (6)
OZALID (OZ (Australia) + A + LID (cover))
32 Dummy's losing head to cocaine and a little pot? (8)
CANNIKIN (MANNIKIN(dummy) with first letter replaced by C (cocaine))
33 Dye that's purple and gold, a streak is found in me (8)
MAUVEINE (ME round AU (gold) + VEIN (streak))
35 Domination in politics; hints of sleaze, scandal, ignominy and shadiness are concealed by corrupt mob (7)
BOSSISM (anag of MOB round SSIS (initial letters) semi &lit)
39 Old prune, or pig pie that's new (6)
PROIGN (anag of OR PIG + N (new))
46 See's city church (4)
ECCE (EC (city) + CE (church))

ZONE THREE
36 Stuffed as pressure increased (6)
PADDED (P (pressure) + ADDED (increased))
43 Nick's training division in New Hampshire (5)
NOTCH (NH (New Hampshire) round OTC (training division))
47 Silliness with third of palace getting involved in prancing of yore (7)
FOOLERY (anag of OF YORE round L (third letter of palace))
51 Mimicking honeycomb stitching, but the first part is omitted (7)
MOCKING (SMOCKING (honeycomb stitching) minus first letter)
54 Chemical element with the addition of revolutionary hydrogen's original (7)
SULPHUR (PLUS (with the addition of) rev + H (hydrogen) + UR (original))
37 At the summit see American finish, but not first (4)
ATOP (A (American) + STOP (finish) minus first letter)
40 Lines upside-down on surgeon's suit (6)
SWORDS (ROWS (lines) rev + DS (surgeon))
48 Aerobatic manoeuvres don't start, I've made a mistake (4)
OOPS (LOOPS (aerobatic manoeuvres) minus first letter)