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Disassembly complete and fully commented!

$80 - System routines

$81 - SRAM, spritemap processing & menus

$82 - Top level main game routines

$83 - FX and door definitions

$84 - PLMs

$85 - Message boxes

$86 - Enemy projectiles

$87 - Animated tiles

$88 - HDMA

$89 - Item PLM graphics, FX loader

$8A - FX tilemaps

$8B - Non gameplay routines

$8C - Title sequence and intro

$8D - Enemy projectile spritemaps, palette FX objects

$8E - Menu tiles

$8F - Rooms definitions

$90 - Samus

$91 - Aran

$92 - Samus animations

$93 - Projectiles

$94 - Block collision, grapple drawing,
      some cutscene graphics

$95..$99 - Cutscene graphics

$9A - Projectile and standard BG3/sprite tiles

$9B - Grapple beam and Samus graphics

$9C - Samus graphics

$9D - Samus graphics

$9E - Samus graphics

$9F - Samus graphics

$A0 - Enemies

$A1 - Enemy population

$A2 - Enemy AI - inc. gunship & shutters

$A3 - Enemy AI - inc. elevator & metroid

$A4 - Enemy AI - Crocomire

$A5 - Enemy AI - Draygon & Spore Spawn

$A6 - Enemy AI - inc. Ridley & zebetites

$A7 - Enemy AI - inc. Kraid & Phantoon

$A8 - Enemy AI - inc. ki-hunter

$A9 - Enemy AI - Mother Brain, Shitroid & dead monsters

$AA - Enemy AI - inc. Torizo & Tourian statue

$AB - Enemy graphics - inc. Kraid

$AC - Enemy graphics - inc. Spore Spawn & Phantoon

$AD - Enemy graphics - Crocomire, gunship & space pirates;
      extra Mother Brain code

$AE - Enemy graphics

$AF - Enemy graphics - inc. Torizo

$B0 - Enemy graphics - inc. Ridley,
      Draygon & Mother Brain

$B1 - Enemy graphics - inc. Shitroid & ki-hunter

$B2 - Enemy AI - space pirates

$B3 - Enemy AI - inc. Botwoon

$B4 - Enemy sets, vulnerabilities, drop chances;
      sprite objects; debug handler

$B5 - Region maps

$B6 - Pause screen graphics

$B7 - Enemy graphics - inc. dead enemies,
      Botwoon & Mother Brain

$B9..$BA - CRE, background images

$BA..$C1 - Tile graphics

$C1..$C2 - Tile tables

$C2..$CE - Palettes, level data

$CF..$DE - Music

$DF - Incomplete unused music

Additional

InsaneFirebat has written an assemblable source code form!