by Andrew Marc Greene
Answer: DON'T FEAR THE REAPER
Problem: Christmas Town/​Halloween Town

This is a variety cryptic in which the down answers must be encrypted using a substitution cipher before being entered into the grid.

This is hinted at in the flavortext—the downworlders are trying to avoid running into a cross, so they have appointed substitutes to appear in their stead.

Once the grid is filled in, the unclued central across entry reads DON’T FEAR THE REAPER, which is the solution to this puzzle.

TAXISHEBREWDANIEL
UNTWISTPWORKSRSSD
TUTAHYWEFTCRYWOLF
LEHISAVEDSTARIUWY
ASPOCKWYOGHDMUFFS
HIEDSAPSHTKYOTOTR
DONTFEARTHEREAPER
FHOZAWADRODDSCHIP
STUDYMQUADMSWEDED
NERAITEMUSTENJETE
ELAPSEDOPALDCAFES
TCSLJZONEDSWANSEA
ADJURERANKLEJNEXT
AcrossClueAnswerExplanation
1Conveyance you can hire to sail against the wind and ocean’s noiseTAXIhomophone for “tack, sea”
4חצי ראש על בירה!—Half-head on beerHEBREWhe(ad) + brew
8Prophet in deal gone wrongDANIELanag.
12Straighten the spine of viscount, wistfullyUNTWISTviscoUNT WISTfully
13Thermodynamic quantity of tungsten or potassiumWORKw + or + k
16“Out ahead” is where to find the location of 19 AUTAHoUT AHead
17You and I, going by foot, make something that looms consumeWEFTwe + ft
18Three emerging from crypt reversed course to scare people with invented threatsCRY WOLFcry + rev. flow
19City in the “French Hawaii”LEHIle + hi
20Like moonwalks, spacewalks commit to long-term storageSAVErev. EVAs
22Taking the mound for the first inning but leaving before the fifth, a marquee player—for example . . .STARstar(ting)
24 . . . Dr. K—falls behind western Rangers et al.SPOCKrev. cops + k
25“Ye Olde” glyph had, at first, been a letter in Middle EnglishYOGHinitials
26Messes up things to keep body parts warmMUFFSdouble def.
27Moved swiftly to camouflage eavesdroppingHIEDhomophone for “hide”
28They’re easily taken from outer Somalia, and one more thingSAPSsa + ps
29Japanese city is satisfied with adopted plaything, in retrospectKYOTOtoy in ok, rev.
38Selection from Berlioz awakens conductorOZAWAberliOZ AWAken
39Dentist follows old line at the PreaknessODDSo + dds
40Nacho ingredient: half a smoked jalapeñoCHIPchip(otle)
41Pay careful attention to hunk at gymSTUDYstud + y
42Quinnipiac University’s academic dormitories, originally a specific area on campusQUADinitials
43Weeds, bananas, and rutabagaSWEDEanag.
45I, returning, met a man with his paramourITEMi + met rev.
46Gun for shooters in Brooklyn evincing recoilSTENnets rev.
48West Side Story character Krupke’s last dance moveJETEjet + e
49Passed by, unexpectedly pleasedELAPSEDanag.
50Hey, buddy, nice stoneOPALo + pal
51Spot for a pot made from California ironCAFEca + fe
52Region of O3 giving off oxygenZONEozone − o
53Welsh city using transposition awes NSASWANSEAanag.
54Strongly impel a spinner; push without gravityADJUREa + dj + ur(g)e
55Gnaw at lower extremity and jointRANKLEr + ankle
5610 embracing 10 on the way back to MIT dorm, colloquiallyNEXTx in ten, rev.

As explained in the flavortext, the down answers rely on a substitution cipher.

down answer letterABCDEFGHIJKLMNOPQRSTUVWXYZ
entered in grid asSILMTBNCPXQUFEDYVHRAWGOZJK

The checked letters in the puzzle are pangrammatic, so by solving all clues the entire cipher can be deduced; although only parts of it are needed to extract the final answer, this allows the entire puzzle to be solved.

DownClueAnswerExplanation
1Choose Megatron to be transformed into solenoidELECTROMAGNETelect + megatron anag.
2Jack, a VI-1 alum, to use the doorbell as a way to show disrespectJEERINGj + ee + ring
3A garment for supporting actor and winner of an Oscar in 1985ABRAHAMa + bra + ham
4Fascinated by sprung trapRAPTanag.
5Huckleberry—one from Northern EuropeFINNdouble def.
6Mowing results in chaos when large Japanese men grab each otherSUMO WRESTLINGanag.
7Decapitated Iditarod participant is eponym for Poe’s houseUSHER(m)usher
9Bugler’s signal when fight is given upTAPSspat rev.
10Become a fountain of tears when fight lost, right?BAWLb(r)awl
11Empathetic groom (not bachelor), fathers, and the People of Israel uncommonly dinedCOMPASSIONATEcom(b) + pas + sion + ate
14Hustle, bustle, and have both a tenant and a landlordSUBLETanag.
15Skill, I agree, involves more than a bit of curiosityACUMENa(cu)men
21Give up most of the way through trivia contest, at bottom of bracketQUITqui(z) + t
22Rave wildly and swearAVERanag.
23#1 baseball card publisher eliminating baseball’s position #1TOPSto(p)ps
31Yank is an architect at churchWRENCHwren + ch
32Formerly about the ear, from another cultureEXOTICex + otic
33Revealed in the mirror: undressed, undressed, undressedNUDErev. hidden
34Southern antique auctioned offSOLDs + old
35Point where there’s no vibration (up-and-down motion) of the head and tail of animalculeNODEnod + e
36Everything in New York is badNAUGHTYn(aught)y
37Fictional MIT alum found in lair on ManhattanIRON MANlaIR ON MANhattan
42Senses using one’s ears, noseKNOWShomophone for nose
44Upwardly mobile poet loses excellent propSTAYy(e)ats rev.
45Howls at the moon in Massachusetts and San Francisco, e.g.BAYSdouble def
46Running the gamut near AustraliaA TO Zat + oz
47Sister captures boy’s heart with part of speechNOUNn(o)un