By John Toomey
Answer: BLACK OPERATION

Six lists have been encoded, as has the title, using a scheme similar to that of standard nautical flags, except that adjacent substitution numbers are summed rather than being represented as standard substitution flags. This is hinted by the puzzle’s substitution flags being in the shape of capital sigmas (Σ). For example, the first five entries in the NATO phonetic alphabet (Alfa, Bravo, Charlie, Delta, Echo) would be encoded as follows:

1
A L F (repeat flag 1)
4
B R (repeat flag 4 (which was itself a repeat of A)) V O
15
C H (repeat flag 7 + rep. 6 + rep. 2 = rep. 15) I E
30
12
D (rep. 16 + rep. 14 = rep. 30) T (rep. 12)
48
(rep. 18 + rep. 10 + rep. 11 + rep. 9 = rep. 48)

(Note that in DELTA, 16 + 14 = 30 refers to the E and L of CHARLIE, and not the 16th and 14th flags, since ARL of CHARLIE is condensed into a single flag.)

The six science and sci-fi themed lists encoded are:

Set D: Medical Professionals = Actors who portrayed The Doctor in Doctor Who:
D.1: HARTNELL
D.2: TROUGHTON
D.3: PERTWEE
D.4: BAKER
D.5: DAVISON
D.6: BAKER
D.7: MCCOY
D.8: MCGANN
D.9: ECCLESTON
D.10: TENNANT
D.11: SMITH
D.12: CAPALDI
D.13: WHITTAKER
Set E: Tiny Pieces = Elements
E.1: HYDROGEN
E.2: HELIUM
E.3: LITHIUM
E.4: BERYLLIUM
E.5: BORON
E.6: CARBON
E.7: NITROGEN
E.8: OXYGEN
E.9: FLOURINE
E.10: NEON
E.11: SODIUM
E.12: MAGNESIUM
E.13: ALUMINUM
E.14: SILICON
E.15: PHOSPHOROUS
E.16: SULFUR
E.17: CHLORINE
E.18: ARGON
E.19: POTASSIUM
E.20: CALCIUM
Set G: Top Talent = Science-Fiction Grandmasters (recipients of the Damon Knight Memorial Grandmaster Award, more specifically)
G.1: HEINLEIN
G.2: WILLIAMSON
G.3: SIMAK
G.4: DECAMP
G.5: LEIBER
G.6: NORTON
G.7: CLARKE
G.8: ASIMOV
G.9: BESTER
G.10: BRADBURY
G.11: DELREY
G.12: POHL
G.13: KNIGHT
G.14: VANVOGT
G.15: VANCE
G.16: ANDERSON
G.17: CLEMENT
G.18: ALDISS
G.19: FARMER
G.20: LEGUIN
Set N: Data Packs = Expansions to the Android: Netrunner card game (aka Data Packs)
N.1: WHATLIESAHEAD
N.2: TRACEAMOUNT
N.3: CYBEREXODUS
N.4: ASTUDYINSTATIC
N.5: HUMANITYSSHADOW
N.6: FUTUREPROOF
N.7: OPENINGMOVES
N.8: SECONDTHOUGHTS
N.9: MALATEMPORA
N.10: TRUECOLORS
N.11: FEARANDLOATHING
N.12: DOUBLETIME
N.13: UPSTALK
N.14: THESPACESBETWEEN
N.15: FIRSTCONTACT
N.16: UPANDOVER
N.17: ALLTHATREMAINS
N.18: THESOURCE
N.19: THEVALLEY
N.20: BREAKERBAY
Set P: Spheres = Planets of our Solar System
P.1: MERCURY
P.2: VENUS
P.3: EARTH
P.4: MARS
P.5: JUPITER
P.6: SATURN
P.7: URANUS
P.8: NEPTUNE
(nobody needs the stress of Pluto’s status, seriously)
Set W: Keep Rolling = Wheel of Time Novels
W.1: THEEYEOFTHEWORLD
W.2: THEGREATHUNT
W.3: THEDRAGONREBORN
W.4: THESHADOWRISING
W.5: THEFIRESOFHEAVEN
W.6: LORDOFCHAOS
W.7: ACROWNOFSWORDS
W.8: THEPATHOFDAGGERS
W.9: WINTERSHEART
W.10: CROSSROADSOFTWILIGHT
W.11: KNIFEOFDREAMS
W.12: THEGATHERINGSTORM
W.13: TOWERSOFMIDNIGHT
W.14: AMEMORYOFLIGHT

These sets can be continued out to (or beyond) the highest reference seen in the equations that follow.

D.8 + N.5 - E.17
= MCGANN + HUMANITYSSHADOW - CHLORINE
= 224 + 572 - 794
= 2
= B

Continuing calculation of the indicated equations results in BLACK OPERATION, the solution.