I still think that theory has backing, ranging from the unused area coordinates in the Lunar core where there Clearly was supposed to be a door at one time, I think it is a reasonable assumption.
Now I have finished recording all scripts in the Overworld (only 90 on the Moon for better or worse)
Basic Script Usage
Overworld/Underworld
Script 1: Nothing
Script 2: Fight (Lots of Things)
Script 3: Target Random Foe, Fight (Lots of Things)
Script 4: Fight, Explode (Bomb, GrayBomb, Balloon)
Script 5: Explode (GrayBomb, Balloon, Grenade, Left Arm, Right Arm)
Script 6: Reaction (Grenade)
Script 7: Target Random Foe, Petrify (Basilisk, BlackLiz)
Script 8: Fight, Petrify (Basilisk, Ice Liz)
Script 9: Petrify (BlackLiz)
Script 10: Target Random Foe, Ice-2 (Ice Liz)
Script 11: Roulette, Fatal (Unused?)
Script 12: Ice-2 (Ice Liz, EvilDoll)
Script 13: Target Random Foe, Beak (Eagle, Roc, Treant)
Script 14: Beak (Cocktric, Roc Baby)
Script 15: Target Random Foe, Fatal (FloatEye, Red Eye, Marion)
Script 16: Fight, Gaze (Red Eye)
Script 17: Target Party, Count, Self-Stop (Unused)
Script 18: Count (Unused)
Script 19: Target Random Foe, Fire1 (Spirit, Soul)
Script 20: Fire1, Fight (Spirit, Soul)
Script 21: Target Random Foe, Sleep (Ghost)
Script 22: Fire2, Fight, Sleep (Ghost)
Script 23: Target Random Foe, Vampire (Cave Bat, Giant Bat, Were Bat, VampGirl, VampLady,)
Script 24: Vampire (Cave Bat, Giant Bat, Were Bat)
Script 25: Self-Peep, 140, 141, Self-Peep, 142, 143, 145, 146, 147, 148, Retreat (Dummy(5))
Script 26: Stop (Treant)
Script 27: Target Random Foe, Bersk (DarkTree)
Script 28: Bersk (DarkTree)
Script 29: Target Random Foe, Needle (SwordRat, Needler, StingRat)
Script 30: Needle (SwordRat, Needler, StingRat)
Script 31: Fatal (TinyMage)
Script 32: Lit-1, Ice-1, Fire1 (TinyMage)
Script 33: Psych (TinyMage, Larva, Crawler)
Script 34: Hold (TinyMage)
Script 35: Fight, Powder (SandMoth, Glomwing, RockMoth)
Script 36: Fight, Heat Ray (Unused?) NOTE: Possibly intended for an unused Moth type?
Script 37: Target All Foes, Quake (Sandpede, Centpede, Arachne)
Script 38: Fight, Quake (Talantla)
Script 39: Quake (Sandpede, Centpede, Arachne, Talantla)
Script 40: Fight, Hug, Fight (Unused) NOTE: Possibly intended for an unused Arachne type.
Script 41: Target All Foes, Tornado (Sandworm)
Script 42: Tornado (Sandworm)
SCript 43: Target All Foes, Wave (Aquaworm)
Script 44: Wave (Aquaworm, Calbrena)
Script 45: Retreat (Red Worm, WaterBug, HugeCell, Officer, General)
Script 46: Vampire (RedWorm, VampGirl, VampLady) NOTE: Repeat of Script 24 and can be replaced.
Script 47: Target Random Foe, Weak (Gargoyle, Hooligan)
Script 48: Fight, Fight, Fight, Weak (Gargoyle)
Script 49: Weak, Fight (Hooligan)
Script 50: Toad (CaveToad, MadToad)
Script 51: Pollen (TrapRose, Cannibal)
Script 52: Chain-Flag1-Search(End), Chain-Disrupt-Flag0(End) (TrapDoor)
Script 53: 139, Tradeoff (TrapDoor)
Script 54: Slow (Crawler, CaveNaga,)
Script 55: Lit-1 (Skelton, Red Bone, Puppet, Milon)
Script 56: Lit-2 (Skull, EvilDoll,)
Script 57: Nothing (Unused)NOTE: A copy of "Nothing", can be replaced.
Script 58: Nothing, Nothing, Fight, Retreat (WaterBug, HugeCell)
Script 59: Remedy (WaterBug, HugeCell)
Script 60: Target All Foes, M-Order, 83, (Officer)
Script 61: 180, 181, Self-Sleep, EndBattl (Dummy(4))
Script 62: Fight, Fight, Fight, Absorb (VampGirl)
Script 63: Fight, Lit-2, Glance (VampLady)
Script 64: Target All Foes, Fire (FlameDog)
Script 65: Fire (FlameDog, D. Machin, Calbrena)
Script 66: Target All Foes, Thunder (Unused) NOTE: Would have likely been used by either an unused ThunderDog or a later Charmed dragon.
Script 67: Thunder (Yellow D., Calbrena)
Script 68: Piggy (Guard)
Script 69: Size (Guard)
Script 70: Wall (BladeMan, EvilDoll)
Script 71: Virus (BladeMan)
Script 72: Enemy Spell - Charm (Lilith)
Script 73: Slap (Lilith)
Script 74: Target Foe, Enemy Spell - Charm (Lamia, Q. Lamia)
Script 75: Fight, Fight, Entangle (Hydra, Python)
Script 76: Peep (Mage)
Script 77: Blast, Drain (Mage)
Script 78: Tongue (Naga)
Script 79: Mute (HugeNaga)
Script 80: Target Random Foe, Bluster (Panther, BlackCat)
Script 81: Bluster (Panther, BlackCat)
Script 82: Absorb (SwordMan)
Script 83: Curse (SwordMan)
Script 84: Ray (Medusa, Gorgon)
Script 85: Target Random Foe, Charm (Dummy(1), Gremlin, Fiend)
Script 86: Fight, Charm, Fight (Dummy(1) NOTE: Was intended for unused Fiend-type foe.
Script 87: Charm (Gremlin, Fiend)
Script 88: Blaze (Chimera, Mantcore)
Script 89: Self-Hatch (Black Liz, Red Worm, HugeNaga, Yellow D., Green D., Lamia)
Script 90: Target All Foes, Blizzard (IceBeast)
Script 91: Blizzard, Fight (IceBeast)
Script 92: Toad(TinyToad) NOTE: Copy of Script 50, can be replaced.
Script 93: Call (Marion, Sorcerer, Conjurer)
Script 94: Target Random Foe, Drain (Roc Larva, Crawler, Sorcerer)
Script 95: Target Random Foe, Warp (Conjurer)
Script 96: Fire1 (Q. Eblan, Puppet)
Script 97: Ice-1 (Puppet)
Script 98: Target All Foes, M-Order, 82 (General)
Script 99: Target Random Foe, Beam (Beamer)
Script 100: Beam (Beamer, Alert, Searcher)
Script 101: Target All Foes, Emission (Unused)
Script 102: Emission (Unused) NOTE: May have been intended for a Beamer-like foe. The only enemy in the game which uses Emission appears to be Dr. Lugae(2)
Script 103: Target Random Foe, Fast (Witch)
Script 104: Slow, Mute (Witch)
Script 105: Self-Toad, Toad, Toad, Self-Toad, Retreat (ToadLady)
Script 106: Target All Foes, M-Order, 138 (ToadLady)
Script 107: Target Random Foe, Stone (Unused) NOTE: This implies that the Warlock was originally intended not to be on the Moon.
Script 108: Fight, Nuke (Unused) NOTE: Whoa. Was this originally intended for the Overworld Warlock?
Script 109: Fire2, Psych, Drain, Fatal (Unused) NOTE: Looks like they may have intended for even more of the Magic Lady-type of foe.
Script 110: Self-Wall (Unused) NOTE: There's more unused Scripts than I thought there would be.
Script 111: Digest (Unused)
Script 112: Fightx2 (Green D., Yellow D., Raven, Roc, Aligator, Crocdile
Script 113: Fight, Thunder (Green D.)
Script 114: Search, Magnet, Search, Beam (LastArm)
Script 115: 9, Nothing (Alert, Searcher)
Script 116: Alert (Alert, Searcher)
Script 117: Breath, Digest, Fight (Molbol)
Script 118: Fight, Fight, Blitz (Unused) NOTE: May have been intended for Clapper's original Attack AI?
Script 119: Blitz (Clapper)
Script 120: Fire2 (EvilDoll)
Script 121: Roulette Laser (Unused) NOTE: An unused sequence also references this.
Script 122: Laser (Unused)
Script 123: Fire, Fight, Fight, Fight, Fight (FlameDog)
Script 124: Magnet (MacGiant)
Script 125: Fission (LastArm)
Script 126: 104, Nothing, 104, Nothing, 104, Nothing, 104, Nothing, 104, Nothing, 104, Nothing, 104, Nothing, 104, Nothing, Fight (Dummy(9)
Script 127: Nothing (Unused)NOTE: A copy of "Nothing" can be replaced.
Script 128: Nothing (Unused)NOTE: Copy, can be replaced.
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Boss Monsters
Script 129: Fight, Fight, Fight, Chain-1-Sprite1-InvinOn-Flag1(End), Nothing, Nothing, Nothing, Chain-2-Sprite0-InvinOff-Flag0(End)(D. Mist)
Script 130: Coldmist, 3,4,5 (D. Mist)
Script 131: 20, Call (Girl)
Script 132: Chain-Sprite67-Quake-EndBattl(End)(Titan)
Script 133: Sprite5, Speed+9, +1Flag, Nothing (OctoMamm)
Script 134: Sprite6, Speed+8, +1Flag, Nothing (OctoMamm)
Script 135: Sprite7, Speed+7, +1Flag, Nothing (OctoMamm)
Script 136: Sprite8, Speed+6, +1Flag, Nothing (OctoMamm)
Script 137: Sprite9, Speed+5, +1Flag, Nothing (OctoMamm)
Script 138: Sprite10, Speed+4, +1Flag, 73, 74 (OctoMamm)
Script 139: Srptie11, Speed+3, +1Flag, Nothing (OctoMamm)
Script 140: +1 Flag, Nothing (OctoMamm)
Script 141: 6, 6, 6, 6, Flag0, (Unused) NOTE: The message just seems to be "Good luck..." over and over again. I guess maybe it's for testing?
Script 142: Flag1 (D. Knight)
Script 143: Counter (Antlion)
Script 144: 23, 24, Flag1, Nothing (Bard)
Script 145: 25, 26, Flag2, Nothing (Bard)
Script 146: 27, 28, Flag3, Nothing (Bard)
Script 147: 29, 30, 22, EndBattl (Bard)
Script 148: C-Anna, 65,66,67,Flag1 (WaterHag(2))
Script 149: 68, R-Images, 69,Flag2, Defense 0% (WaterHag(2))
Script 150: 70, Self-Vanish (WaterHag(2))
Script 151: 64, Chain-Explode-TradeOff(End) (MomBomb)
Script 152: Sprite13, Flag1, Nothing(MomBomb)
Script 153: Nothing, 8, Target All Foes, M-Order, Nothing (Milon)
Script 154: Lit-1, Fight (Milon)
Script 155: 7, Self-Vanish (Milon)
Script 156: Drain (Ghast)
Script 157: 21, 36, Flag1 (Milon-Z)
Script 158: 171, DullSong (Unused) NOTE: Was likely meant for Milon-Z as a counter.
Script 159: Dark, Dark, Dark, 33, 34, 35, 149, Self-Vanish (D. Knight)
Script 160: Dark, 32, Flag0 (D. Knight)
Script 161: Entangle, Fight (Left Arm)
Script 162: Vampire (RightArm) NOTE: This is a copy of Scripts 24 and 46 and can be replaced.
Script 163: Fight, Fight, Fight, Fight, Target All Foes, Fast, Fight (Baigan)
Script 164: Target All KO Foes, Recover (Baigan)
Script 165: Self-Wall (Baigan) NOTE: This is a copy of Script 110, which is an unused Script.
Script 166: Chain-Reaction1-71-Sprite19-WeakBolt(End), Nothing, Wave, Self-Fast (Kainazzo)
Script 167: Defense+, Flag1, Nothing (Kainazzo)
Script 168: Fight, Flag1
Script 169: Chain-Flag0-Reaction0-Sprite18-WeakIce-117(End)(Kainazzo)
Script 170: Chain-Flag2-Reaction0-Sprite20-WeakIce-72-Nothing(End)(Kainazzo)
Script 171: Nothing, Nothing,, Nothing, 10, Chain-Fire2-Lit-2-Ice-2(End), Weak,11,12,13, EndBattl(Dark Elf(1))
Script 172: 45, Fight, Fight, Fight, Fight, Fight, Quake (DarkElf(1))
Script 173: Chain-Fire2-Lit-2-Ice-2(End), Weak, Whisper (DarkElf(2))
Script 174: Chain-14-Music(Boss)-TradeOff(End) (DarkElf(2))
Script 175: D. Breath (DarkElf(3))
Script 176: Target-Type2, Wall (Sandy)
Script 177: Berserk, Slow, AllFoes-Cure2 (Sandy)
Script 178: 102, 103, Target-Type2, Fire2, 102,103, Target-Type2, Lit-2, 102, 103, Target-Type2, Ice-2, 102, 103, Target-Type2, 102, 103, Virus (Mindy)
Script 179: Fire1, Lit-1, Ice-1, Venom (Mindy)
Script 180: 46, Fight (Cindy)
Script 181: Fight, AllFoes-Remedy(Cindy)
Script 182: Chain-Weak-Ray(End), Fight (Valvalis)
Script 183: Fight, Nothing, Flag0 (Valvalis)
Script 184: Chain-Defense+, M Defense+, Flag1, Sprite22(End) (Valvalis)
Script 185: Sprite21, Flag2, Defense-, M. Defense -, Fight (Valvalis)
Script 186: 47,48,Nothing (Valvalis)
Script 187: 15, Target-DarkKn, Fight, 16, Kick, 17, Target-DarkKn, Fight, 18, Kick, Flag1 (Karate)
Script 188: 19, EndBattl (Karate)
Script 189: 127, Music(Calcobrena), TradeOff (Calbrena)
Script 190: 126, Music(Boss), TradeOff (Cal, Brena)
Script 191: 106, 108, Sprite17, Glare (Rubicant)
Script 192: Chain-Sprite19-ResistNone-VeryWeakIce(End), Glare, Chain-Sprite16,ResistIceAbsorb-WeakIceAbsorb(End), Chain-Sprite17-None-VeryWeakIce(End) Chain-Sprite16-ResistIceAbsorb-WeakIceAbsorb(End), Flag1 (Rubicant)
Script 193: TargetAllies-Life1 (Rubicant)
Script 194: TargetAllies-Fire2 (Rubicant)
Script 195: 144, 107, 6, Self-Vanish (Rubicant)
Script 196: 49, 50, Nothing, Fire2, 51, 52, Nothing, Fire2, Fire2, 53, Nothing, UNKNOWN, Music(Sad), Target-Type2, M-Order, Sprite31, Flag1, 55, Nothing 56, Nothing, 57, Nothing, 58, Nothing, 109, Nothing, 110, Nothing, 111, Nothing, 112, Nothing, 113, Nothing, Self-Vanish(K. Eblan)
Script 197: 115, 116, Self-Vanish (Q. Eblan)
Script 198: 96, 54, Nothing (Q. Eblan)
Script 199: Chain-88-89-Nothing-Flag1(End) (Dr. Lugae(1))
Script 200: Chain-96-TargetType2-Heal-89(End), Nothing (Dr. Lugae(1))
Script 201: 94, 95, TradeOff, Flag0 (Dr. Lugae(1))
Script 202: 90, 91, 89,92, Flag2, Nothing (Dr. Lugae(1))
Script 203: 97, Explode (Balnab)
Script 204: TargetType2-Fight, Flag2 (Balnab)
Script 205: Fight, Fight, 100, Explode (Balnab-Z)
Script 206: 98, Chain-99-40-Music(Boss)-Flag1-Poison(End) (Dr. Lugae(2))
Script 207: Beam, Laser, Emission, TargetAllies-Heal (Dr. Lugae(2))
Script 208: Gas (Dr. Lugae(2))
SCript 209: Crush, Nothing (EvilWall)
Script 210: Chain-WallMove-Fight+1Flag(End) (EvilWall)
Script 211: Petrify (EvilWall) NOTE: Copy of Script9, can be replaced.
Script 212: Fight, Fight, Fight, Sprite43, Nothing, Nothing, Odin, Fight, Fight, Sprite43, Nothing, Nothing, Odin, Fight, Chain-Sprite43-Flag1(End), Flag0, Odin (Odin)
Script 213: 105, Self-Vanish (Odin)
Script 214: Chain-Sprite45-Nothing-BigWave(End), Sprite46, Nothing, Ice-2, Ice-2, Nothing, Chain-Sprite45-BigWave(End), Sprite46, Nothing, Ice-2, Nothing (Leviatan)
Script 215: TargetAllies-Maser (Leviatan, Attacker)
Script 216: TargetType1-Remedy (Defender)
Script 217: 121, Nothing, 122, Nothing, 123, Nothing, 124, Nothing, 125, Chain-Sprite48-MegaNuke(End), Wait, Sprite47 (Unused)NOTE: It is clearly a copy of Bahamut's Moon Script, but as this is referenced in the Overworld section, it goes completely unused.
Script 218: 59, 60, Jump, Nothing, 61, 62, Flag1 (Dragoon)
Script 219: Jump (Dragoon)
Script 220: Chain-63-Jump-EndBattl(End) (Dragoon)
Script 221: 43, 44, Nothing (Golbez(1))
Script 222: 37, 38, 39, 40, 41, Nothing (Golbez(1))
Script 223: 42, Self-Vanish (Golbez(1))
Script 224: Nothing, Nothing, Chain-75-76-Nothing-77-Hold Gas-78-79-Nothing-80-Call-Flag1-Nothing(End) (Golbez(2))
Script 225: Nothing (Golbez(2)) NOTE:A copy of Script1 and can be replaced.
Script 226: 84, 177, Heal, 85, 86, Wait, Music(Decisive), G-Rydia, Flag2 (Golbez(2))
Script 227: Virus, Lit-3, Fire-2 (Golbez(2))
Script 228: 87, Self-Vanish (Golbez(2)
Script 229: Chain-Yang2-Demolish-Kain2-Demolish-Rosa2-Demolish(End) Chain-81-Nothing-InvinOff-G-MistD-G-MD-Spl(End) (Shadow)
Script 230: Self-Cure4, Flag1 (Asura)
Script 231: Self-Cure3, Flag2 (Asura)
Script 232: Life1, Flag0 (Asura)
Script 233: Sprite55, Sprite53, Sprite54, Sprite55, Flag2, Fight (Asura)
Script 234: Sprite54, Sprite55, Sprite53, Sprite54, Flag0, Fight (Asura)
Script 235: Sprite53, Sprite54, Sprite55, Sprite53, Flag1, Fight (Asura)
Script 236: ResistIceBolt, VeryWeakFire, Chain-RaceZombie(End), Fight, Fight, Fight, Fight, Curse (Elements(1))
Script 237: Flag1, Sprite17, ResistFireBolt, VeryWeakIce, RaceMage (Elements(1))
Script 238: TargetAllies-Fire2, TargetAllies-Fire3, TargetAllies-Glare (Elements(1))
Script 239: Tradeoff (Elements(1))
Script 240: Chain-ResistFireIce-VeryWeakBolt-RaceNone(End), Fight, Fight, Fight, Fight, BigWave (Elements(2))
Script 241: Flag3, Sprite116, ResistNone, WeakHoly, RaceNone, Nothing (Elements(2))
Script 242: Ray, Fight, Ray, Fight, Storm, (Elements(2))
Script 243: Self-Wall (CPU) NOTE: This is a copy of Script 110 which is an unused script and can be changed.
Script 244: Globe199, Globe199, TargetKOFoes-Recover (CPU)
Script 245: Fight, Glance, Fight, Fight, Hold, Fight (Calbrena)
Script 246: Chain-Fight-Fight(End), Nothing, Flag0, Nothing (Rubicant)
Script 247: Ice-2 (Unused) NOTE: Copy of Script12.
Script 248: Self-Wall, Flag1 (Unused) NOTE: Copy of an already unused Moon Script for Bahamut.
Script 249: Blaze, Fight, Fight (Mantcore)
Script 250: 174, 175, EXplode (Dummy(3))
Script 251: 151, 152, 153, EndBattl (Dummy(6))
Script 252: Music(Fabul), UNKNOWN, 182, Nothing, Nothing, Nothing, 183, Vanish (Dummy(7))
Script 253: 184, 185, 186, EndBattl (Dummy(8))
Script 254: 119, Slap (Dummy(7))
Script 255: Empty (Unused)
I should hopefully finish the Moon scripts soon as well.