diff --git a/.make_hackeroot.mk b/.make_hackeroot.mk
index cd7247dde..530d530a3 100644
--- a/.make_hackeroot.mk
+++ b/.make_hackeroot.mk
@@ -1,29 +1,195 @@
-# Set prefix to mips binutils binaries (mips-linux-gnu-ld => 'mips-linux-gnu-') - Change at your own risk!
-# In nearly all cases, not having 'mips-linux-gnu-*' binaries on the PATH is indicative of missing dependencies
+#### Compiling ####
 
 # Returns the path to the command $(1) if exists. Otherwise returns an empty string.
 find-command = $(shell which $(1) 2>/dev/null)
 
+# Set prefix to mips binutils binaries (mips-linux-gnu-ld => 'mips-linux-gnu-') - Change at your own risk!
+# In nearly all cases, not having 'mips-linux-gnu-*' binaries on the PATH is indicative of missing dependencies
 ifneq ($(call find-command,mips-n64-ld),)
-  MIPS_BINUTILS_PREFIX := mips-n64-
+	MIPS_BINUTILS_PREFIX := mips-n64-
 else ifneq ($(call find-command,mips64-ld),)
-  MIPS_BINUTILS_PREFIX := mips64-
+	MIPS_BINUTILS_PREFIX := mips64-
 else ifneq ($(call find-command,mips-linux-gnu-ld),)
-  MIPS_BINUTILS_PREFIX := mips-linux-gnu-
+	MIPS_BINUTILS_PREFIX := mips-linux-gnu-
 else ifneq ($(call find-command,mips64-linux-gnu-ld),)
-  MIPS_BINUTILS_PREFIX := mips64-linux-gnu-
+	MIPS_BINUTILS_PREFIX := mips64-linux-gnu-
 else ifneq ($(call find-command,mips-ld),)
-  MIPS_BINUTILS_PREFIX := mips-
+	MIPS_BINUTILS_PREFIX := mips-
 else ifneq ($(call find-command,mips64-elf-ld),)
-  MIPS_BINUTILS_PREFIX := mips64-elf-
+	MIPS_BINUTILS_PREFIX := mips64-elf-
 else
-  $(error Unable to detect a suitable MIPS toolchain installed)
+	$(error Unable to detect a suitable MIPS toolchain installed)
+endif
+
+# Enable optimization flags to use GDB on Ares
+# Default value: `0`
+ARES_GDB := 0
+
+# Toggle release or debug mode. 1=Release, 0=Debug
+# Default value: `0`
+RELEASE := 0
+
+# Compression algorithm. Valid algorithms are 'yaz', 'lzo' and 'aplib'
+# Default value: `yaz`
+COMPRESSION ?= yaz
+COMPRESSION_TYPE ?= $(shell echo $(COMPRESSION) | tr '[:lower:]' '[:upper:]')
+
+# Platform compatibility flags
+# Default value: (nothing)
+TARGET ?=
+ifeq ($(TARGET),wad)
+CFLAGS := -fno-reorder-blocks -fno-optimize-sibling-calls
+CPP_DEFINES := -DCONSOLE_WIIVC
+else ifeq ($(TARGET),iso)
+CFLAGS := -fno-reorder-blocks -fno-optimize-sibling-calls
+CPP_DEFINES := -DCONSOLE_GC
+endif
+
+# Set PACKAGE_VERSION define for printing commit hash
+ifeq ($(origin PACKAGE_VERSION), undefined)
+	PACKAGE_VERSION := $(shell git log -1 --pretty=%h | tr -d '\n')
+	ifeq ('$(PACKAGE_VERSION)', '')
+		PACKAGE_VERSION = Unknown version
+	endif
+endif
+
+# Define author and package version for every OoT version
+CPP_DEFINES += -DPACKAGE_VERSION='$(PACKAGE_VERSION)' -DCOMPRESS_$(COMPRESSION_TYPE)=1
+OPTFLAGS += -ffast-math -fno-unsafe-math-optimizations
+
+# Override optimization flags if using GDB
+ifeq ($(ARES_GDB),1)
+	OPTFLAGS := -Og -ggdb3
+endif
+
+#### Tools ####
+
+FLIPS      := tools/Flips/flips
+GZINJECT   := tools/gzinject/gzinject
+
+# Temporary measure to avoid issues on ISO builds (same for `CFLAGS_IDO`).
+# The real fix would be having the proper fixes in the N64 emulator itself
+# but this requires some time to figure it out.
+CC_IDO     := tools/ido_recomp/linux/5.3/cc
+
+#### Files ####
+
+# Config file used for building ISOs.
+DMA_CONFIG_FILE := dma_config.txt
+
+# Baserom to use when creating BPS patches
+BASEROM_PATCH ?= baseroms/$(VERSION)/baserom.z64
+
+#### Build Rules ####
+
+# Build the codebase to inject in a WAD file (for Wii VC)
+# Steps:
+#		- check if there's the common-key.bin file
+#		- build and compress the rom
+#		- inject the binary in the wad file (and apply patches)
+#		- remove temporary folders
+wad:
+	$(call print,Patching WAD...)
+ifeq ("$(wildcard baseroms/$(VERSION)/common-key.bin)", "")
+	$(error Please provide the common-key.bin file.)
 endif
+	$(V)$(MAKE) compress TARGET=wad
+	$(V)$(GZINJECT) -a inject -r 1 -k baseroms/$(VERSION)/common-key.bin -w baseroms/$(VERSION)/basewad.wad -m $(ROMC) -o $(WAD) -t "HackerOoT" -i NHOE -p tools/gzinject/patches/NACE.gzi -p tools/gzinject/patches/gz_default_remap.gzi
+	$(V)$(RM) -r wadextract/
+	$(call print,Success!)
+
+# Build the codebase to inject in a ISO file (for GameCube)
+# Steps:
+#		- build and compress the rom
+#		- create the dma config file
+#		- extract the iso
+#		- copy the rom and dma config file to the extracted iso folder
+#		- remove any unnecessary files
+#		- apply the modifications on the emulator binary
+#		- pack the iso
+#		- remove temporary folders
+iso:
+	$(V)$(MAKE) compress TARGET=iso
+	$(call print,Patching ISO...)
+	$(V)$(PYTHON) tools/gc_utility.py -v $(VERSION) -c $(COMPRESSION)
+	$(V)$(GZINJECT) -a extract -s baseroms/$(VERSION)/baseiso.iso
+	$(V)cp $(BUILD_DIR)/$(DMA_CONFIG_FILE) isoextract/zlj_f.tgc/$(DMA_CONFIG_FILE)
+	$(V)cp $(ROMC) isoextract/zlj_f.tgc/zlj_f.n64
+	$(V)$(RM) -r isoextract/S_*.tgc/ isoextract/zlj_f.tgc/*.thp
+	$(V)$(FLIPS) --apply tools/gamecube.bps isoextract/zlj_f.tgc/main.dol isoextract/zlj_f.tgc/main.dol
+	$(V)$(GZINJECT) -a pack -s $(ISO)
+	$(V)$(RM) -r isoextract/
+	$(call print,Success!)
+
+# Create a BPS patch for the built rom
+# Steps:
+#		- run Flips and create the patch
+# TODO: add compressed rom support.
+patch:
+	$(call print,Creating BPS patch...)
+	$(V)$(FLIPS) --create --bps $(BASEROM_PATCH) $(ROM) $(BPS)
+	$(call print,Success!)
+
+# Create F3DEX3 bps patches
+# Steps:
+#		- run Flips and create the patches
+create_f3dex3_patches: F3DEX3/f3dzex2.code F3DEX3/f3dzex2.data
+	$(call print,Creating F3DEX3 patches...)
+	$(V)$(FLIPS) --create --bps F3DEX3/f3dzex2.code F3DEX3/F3DEX3_BrW.code F3DEX3/F3DEX3_BrW.code.bps
+	$(V)$(FLIPS) --create --bps F3DEX3/f3dzex2.data F3DEX3/F3DEX3_BrW.data F3DEX3/F3DEX3_BrW.data.bps
+	$(V)$(FLIPS) --create --bps F3DEX3/f3dzex2.code F3DEX3/F3DEX3_BrW_PA.code F3DEX3/F3DEX3_BrW_PA.code.bps
+	$(V)$(FLIPS) --create --bps F3DEX3/f3dzex2.data F3DEX3/F3DEX3_BrW_PA.data F3DEX3/F3DEX3_BrW_PA.data.bps
+	$(V)$(FLIPS) --create --bps F3DEX3/f3dzex2.code F3DEX3/F3DEX3_BrW_PB.code F3DEX3/F3DEX3_BrW_PB.code.bps
+	$(V)$(FLIPS) --create --bps F3DEX3/f3dzex2.data F3DEX3/F3DEX3_BrW_PB.data F3DEX3/F3DEX3_BrW_PB.data.bps
+	$(V)$(FLIPS) --create --bps F3DEX3/f3dzex2.code F3DEX3/F3DEX3_BrW_PC.code F3DEX3/F3DEX3_BrW_PC.code.bps
+	$(V)$(FLIPS) --create --bps F3DEX3/f3dzex2.data F3DEX3/F3DEX3_BrW_PC.data F3DEX3/F3DEX3_BrW_PC.data.bps
+	$(V)$(FLIPS) --create --bps F3DEX3/f3dzex2.code F3DEX3/F3DEX3_BrW_NOC.code F3DEX3/F3DEX3_BrW_NOC.code.bps
+	$(V)$(FLIPS) --create --bps F3DEX3/f3dzex2.data F3DEX3/F3DEX3_BrW_NOC.data F3DEX3/F3DEX3_BrW_NOC.data.bps
+	$(V)$(FLIPS) --create --bps F3DEX3/f3dzex2.code F3DEX3/F3DEX3_BrW_NOC_PA.code F3DEX3/F3DEX3_BrW_NOC_PA.code.bps
+	$(V)$(FLIPS) --create --bps F3DEX3/f3dzex2.data F3DEX3/F3DEX3_BrW_NOC_PA.data F3DEX3/F3DEX3_BrW_NOC_PA.data.bps
+	$(V)$(FLIPS) --create --bps F3DEX3/f3dzex2.code F3DEX3/F3DEX3_BrW_NOC_PB.code F3DEX3/F3DEX3_BrW_NOC_PB.code.bps
+	$(V)$(FLIPS) --create --bps F3DEX3/f3dzex2.data F3DEX3/F3DEX3_BrW_NOC_PB.data F3DEX3/F3DEX3_BrW_NOC_PB.data.bps
+	$(V)$(FLIPS) --create --bps F3DEX3/f3dzex2.code F3DEX3/F3DEX3_BrW_NOC_PC.code F3DEX3/F3DEX3_BrW_NOC_PC.code.bps
+	$(V)$(FLIPS) --create --bps F3DEX3/f3dzex2.data F3DEX3/F3DEX3_BrW_NOC_PC.data F3DEX3/F3DEX3_BrW_NOC_PC.data.bps
+	$(call print,Success!)
+
+# Build the rom and print its checksum (using md5)
+# Steps:
+#		- run `make clean`
+#		- build the rom
+#		- show the checksum
+verify:
+	$(V)$(MAKE) clean
+	$(V)$(MAKE) rom
+	@md5sum $(ROM)
+
+.PHONY: wad iso patch create_f3dex3_patches verify
+
+F3DEX3/f3dzex2.code:
+	$(V)dd bs=1 if=$(BASEROM_DIR)/baserom-decompressed.z64 of=$@ skip=12374256 count=5680 status=none
+
+F3DEX3/f3dzex2.data:
+	$(V)dd bs=1 if=$(BASEROM_DIR)/baserom-decompressed.z64 of=$@ skip=12379936 count=1056 status=none
+
+F3DEX3/F3DEX3%.code: F3DEX3/F3DEX3%.code.bps F3DEX3/f3dzex2.code
+	$(V)$(FLIPS) --apply F3DEX3/F3DEX3$*.code.bps F3DEX3/f3dzex2.code $@
+	
+F3DEX3/F3DEX3%.data: F3DEX3/F3DEX3%.data.bps F3DEX3/f3dzex2.data
+	$(V)$(FLIPS) --apply F3DEX3/F3DEX3$*.data.bps F3DEX3/f3dzex2.data $@
+
+.PRECIOUS: $(UCODE_FILES)
+
+$(BUILD_DIR)/F3DEX3/%.o: F3DEX3/%
+	$(call print,Wrapping binary to ELF:,$<,$@)
+	$(V)mkdir -p $(BUILD_DIR)/F3DEX3
+	$(V)$(OBJCOPY) -I binary -O elf32-big $< $@
+
+#### Output ####
 
 # Verbose toggle
 V := @
 ifeq (VERBOSE, 1)
-    V=
+	V=
 endif
 
 # Colors
@@ -37,27 +203,5 @@ PRINT := printf
 
 # Generic print function for make rules
 define print
-  $(V)echo -e "$(GREEN)$(1) $(YELLOW)$(2)$(GREEN) -> $(BLUE)$(3)$(NO_COL)"
+	$(V)echo -e "$(GREEN)$(1) $(YELLOW)$(2)$(GREEN) -> $(BLUE)$(3)$(NO_COL)"
 endef
-
-# Enable optimization flags to use GDB on Ares
-ARES_GDB := 1
-
-# Toggle release or debug mode. 1=Release, 0=Debug
-# Note: currently only used for HackerOoT
-RELEASE := 0
-
-# Valid compression algorithms are 'yaz', 'lzo' and 'aplib'
-COMPRESSION ?= yaz
-COMPRESSION_TYPE ?= $(shell echo $(COMPRESSION) | tr '[:lower:]' '[:upper:]')
-
-# Platform compatibility flags
-TARGET ?=
-
-ifeq ($(TARGET),wad)
-CFLAGS := -DCONSOLE_WIIVC -fno-reorder-blocks -fno-optimize-sibling-calls
-CPPFLAGS := -DCONSOLE_WIIVC
-else ifeq ($(TARGET),iso)
-CFLAGS := -DCONSOLE_GC -fno-reorder-blocks -fno-optimize-sibling-calls
-CPPFLAGS := -DCONSOLE_GC
-endif
diff --git a/Makefile b/Makefile
index 44ed14fa1..0267d87f0 100644
--- a/Makefile
+++ b/Makefile
@@ -13,9 +13,6 @@ SHELL = /bin/bash
 
 -include .make_options.mk
 
-# HackerOoT options
--include .make_hackeroot.mk
-
 COMPILER ?= gcc
 
 # Target game version. Ensure the corresponding input ROM is placed in baseroms/$(VERSION)/baserom.z64.
@@ -54,6 +51,16 @@ N64_EMULATOR ?=
 # of the debug ROM for better emulator compatibility, or to build US versions of NTSC N64 ROMs.
 # REGION ?= US
 
+PROJECT_DIR := $(dir $(realpath $(firstword $(MAKEFILE_LIST))))
+BUILD_DIR := build/$(VERSION)
+EXPECTED_DIR := expected/$(BUILD_DIR)
+BASEROM_DIR := baseroms/$(VERSION)
+EXTRACTED_DIR := extracted/$(VERSION)
+VENV := .venv
+
+# Add HackerOoT options
+-include .make_hackeroot.mk
+
 CFLAGS ?=
 CPPFLAGS ?=
 CFLAGS_IDO ?=
@@ -121,43 +128,20 @@ else ifeq ($(VERSION),gc-jp-ce)
 else ifeq ($(VERSION),hackeroot-mq)
   REGION := NULL
   PLATFORM := GC
-  PAL := 1
-  MQ := 1
   DEBUG := 1
 else
 $(error Unsupported version $(VERSION))
 endif
 
-ifeq ($(VERSION),hackeroot-mq)
-  HACKEROOT := 1
-else
-  HACKEROOT := 0
-endif
-
 ifeq ($(COMPILER),gcc)
   CPP_DEFINES += -DCOMPILER_GCC -DNON_MATCHING -DAVOID_UB -std=gnu11
 else
   $(error Unsupported compiler. Please use gcc as the COMPILER variable.)
 endif
 
-PROJECT_DIR := $(dir $(realpath $(firstword $(MAKEFILE_LIST))))
-BUILD_DIR := build/$(VERSION)
-EXPECTED_DIR := expected/$(BUILD_DIR)
-BASEROM_DIR := baseroms/$(VERSION)
-EXTRACTED_DIR := extracted/$(VERSION)
-VENV := .venv
-
 MAKE = make
 CPPFLAGS += -P -xc -fno-dollars-in-identifiers
 
-# Set PACKAGE_VERSION define for printing commit hash
-ifeq ($(origin PACKAGE_VERSION), undefined)
-  PACKAGE_VERSION := $(shell git log -1 --pretty=%h | tr -d '\n')
-  ifeq ('$(PACKAGE_VERSION)', '')
-    PACKAGE_VERSION = Unknown version
-  endif
-endif
-
 # Converts e.g. ntsc-1.0 to NTSC_1_0
 ifeq ($(VERSION),hackeroot-mq)
 CPP_DEFINES += -DOOT_VERSION=GC_EU_MQ_DBG
@@ -176,7 +160,6 @@ else
 endif
 
 ifeq ($(VERSION),hackeroot-mq)
-  CPP_DEFINES += -DENABLE_HACKEROOT=1
   OPTFLAGS := -Os
 
   ifeq ($(RELEASE),1)
@@ -193,22 +176,8 @@ else
     CPP_DEFINES += -DNDEBUG -DOOT_DEBUG=0
     OPTFLAGS := -O2 -g3
   endif
-
-  CPP_DEFINES += -DENABLE_HACKEROOT=0
-endif
-
-# Override optimization flags if using GDB
-ifeq ($(ARES_GDB),1)
-  OPTFLAGS := -Og -ggdb3
 endif
 
-# Define author and package version for every OoT version
-# Note: this won't be used if not using HackerOoT
-CFLAGS += -DPACKAGE_VERSION='$(PACKAGE_VERSION)' -DCOMPRESS_$(COMPRESSION_TYPE)=1
-CPPFLAGS += -DPACKAGE_VERSION='$(PACKAGE_VERSION)' -DCOMPRESS_$(COMPRESSION_TYPE)=1
-CFLAGS_IDO += -DPACKAGE_VERSION='$(PACKAGE_VERSION)' -DCOMPRESS_$(COMPRESSION_TYPE)=1
-OPTFLAGS += -ffast-math -fno-unsafe-math-optimizations
-
 ifeq ($(OS),Windows_NT)
     DETECTED_OS=windows
 else
@@ -255,9 +224,6 @@ ELF2ROM    := tools/elf2rom
 ZAPD       := tools/ZAPD/ZAPD.out
 FADO       := tools/fado/fado.elf
 PYTHON     ?= $(VENV)/bin/python3
-FLIPS      := tools/Flips/flips
-GZINJECT   := tools/gzinject/gzinject
-CC_IDO     := tools/ido_recomp/linux/5.3/cc
 
 # Command to replace $(BUILD_DIR) in some files with the build path.
 # We can't use the C preprocessor for this because it won't substitute inside string literals.
@@ -310,18 +276,19 @@ else
   ROM      := $(BUILD_DIR)/oot-$(VERSION).z64
 endif
 ROMC     := $(ROM:.z64=-compressed-$(COMPRESSION).z64)
-WAD      := $(ROM:.z64=.wad)
-ISO      := $(ROM:.z64=.iso)
-BPS      := $(ROM:.z64=.bps)
 ELF      := $(ROM:.z64=.elf)
 MAP      := $(ROM:.z64=.map)
 LDSCRIPT := $(ROM:.z64=.ld)
-DMA_CONFIG_FILE := dma_config.txt
 # description of ROM segments
 SPEC := spec
 
-# Baserom to use when creating BPS patches
-BASEROM_PATCH ?= baseroms/$(VERSION)/baserom.z64
+# HackerOoT files
+WAD      := $(ROM:.z64=.wad)
+ISO      := $(ROM:.z64=.iso)
+BPS      := $(ROM:.z64=.bps)
+UCODE_PATCHES := $(wildcard F3DEX3/*.bps)
+UCODE_FILES   := $(foreach f,$(UCODE_PATCHES:.bps=),$f)
+UCODE_O_FILES := $(foreach f,$(UCODE_FILES),$(BUILD_DIR)/$f.o)
 
 ifeq ($(COMPILER),gcc)
 SRC_DIRS := $(shell find src -type d)
@@ -420,10 +387,6 @@ O_FILES       := $(foreach f,$(S_FILES:.s=.o),$(BUILD_DIR)/$f) \
                  $(foreach f,$(BASEROM_BIN_FILES),$(BUILD_DIR)/baserom/$(notdir $f).o) \
                  $(BUILD_DIR)/src/code/z_message_z_game_over.o
 
-UCODE_PATCHES := $(wildcard F3DEX3/*.bps)
-UCODE_FILES   := $(foreach f,$(UCODE_PATCHES:.bps=),$f)
-UCODE_O_FILES := $(foreach f,$(UCODE_FILES),$(BUILD_DIR)/$f.o)
-
 OVL_RELOC_FILES := $(shell $(CPP) $(CPPFLAGS) $(SPEC) | $(BUILD_DIR_REPLACE) | grep -o '[^"]*_reloc.o' )
 
 # Automatic dependency files
@@ -469,12 +432,14 @@ ifeq ($(COMPILER),gcc)
   $(BUILD_DIR)/src/libultra/libc/ll.o: OPTFLAGS := -Ofast
   $(BUILD_DIR)/src/overlays/%.o: CFLAGS += -fno-merge-constants -mno-explicit-relocs -mno-split-addresses
 
+## HackerOoT overrides ##
+
   $(BUILD_DIR)/src/overlays/actors/ovl_Item_Shield/%.o: OPTFLAGS := -O2
   $(BUILD_DIR)/src/overlays/actors/ovl_En_Part/%.o: OPTFLAGS := -O2
   $(BUILD_DIR)/src/overlays/actors/ovl_Item_B_Heart/%.o: OPTFLAGS := -O0
   $(BUILD_DIR)/src/overlays/actors/ovl_Bg_Mori_Hineri/%.o: OPTFLAGS := -O0
 
-# library overrides for Gamecube
+# library overrides
 ifeq ($(TARGET),iso)
   MIPS_VERSION_IDO := -mips2
   CFLAGS_IDO += -G 0 -non_shared -fullwarn -verbose -Xcpluscomm $(INC) -Wab,-r4300_mul -woff 516,609,649,838,712
@@ -503,6 +468,7 @@ ifeq ($(TARGET),iso)
   $(BUILD_DIR)/src/libultra/os/aisetnextbuf.o: CFLAGS := $(CFLAGS_IDO)
   $(BUILD_DIR)/src/libultra/os/aisetnextbuf.o: CC := $(CC_IDO)
 endif
+
 endif
 
 #### Main Targets ###
@@ -522,29 +488,6 @@ compress:
 	$(V)$(MAKE) $(ROMC)
 	$(call print,Success!)
 
-wad:
-	$(call print,Patching WAD...)
-ifeq ("$(wildcard baseroms/$(VERSION)/common-key.bin)", "")
-	$(error Please provide the common-key.bin file.)
-endif
-	$(V)$(MAKE) compress TARGET=wad
-	$(V)$(GZINJECT) -a inject -r 1 -k baseroms/$(VERSION)/common-key.bin -w baseroms/$(VERSION)/basewad.wad -m $(ROMC) -o $(WAD) -t "HackerOoT" -i NHOE -p tools/gzinject/patches/NACE.gzi -p tools/gzinject/patches/gz_default_remap.gzi
-	$(V)$(RM) -r wadextract/
-	$(call print,Success!)
-
-iso:
-	$(V)$(MAKE) compress TARGET=iso
-	$(call print,Patching ISO...)
-	$(V)$(PYTHON) tools/gc_utility.py -v $(VERSION) -c $(COMPRESSION)
-	$(V)$(GZINJECT) -a extract -s baseroms/$(VERSION)/baseiso.iso
-	$(V)cp $(BUILD_DIR)/$(DMA_CONFIG_FILE) isoextract/zlj_f.tgc/$(DMA_CONFIG_FILE)
-	$(V)cp $(ROMC) isoextract/zlj_f.tgc/zlj_f.n64
-	$(V)$(RM) -r isoextract/S_*.tgc/ isoextract/zlj_f.tgc/*.thp
-	$(V)$(FLIPS) --apply tools/gamecube.bps isoextract/zlj_f.tgc/main.dol isoextract/zlj_f.tgc/main.dol
-	$(V)$(GZINJECT) -a pack -s $(ISO)
-	$(V)$(RM) -r isoextract/
-	$(call print,Success!)
-
 clean:
 	$(V)$(RM) -r $(BUILD_DIR)
 	$(call print,Success!)
@@ -592,38 +535,7 @@ ifeq ($(N64_EMULATOR),)
 endif
 	$(N64_EMULATOR) $(ROM)
 
-patch:
-	$(call print,Creating BPS patch...)
-	$(V)$(FLIPS) --create --bps $(BASEROM_PATCH) $(ROM) $(BPS)
-	$(call print,Success!)
-
-create_f3dex3_patches: F3DEX3/f3dzex2.code F3DEX3/f3dzex2.data
-	$(call print,Creating F3DEX3 patches...)
-	$(V)$(FLIPS) --create --bps F3DEX3/f3dzex2.code F3DEX3/F3DEX3_BrW.code F3DEX3/F3DEX3_BrW.code.bps
-	$(V)$(FLIPS) --create --bps F3DEX3/f3dzex2.data F3DEX3/F3DEX3_BrW.data F3DEX3/F3DEX3_BrW.data.bps
-	$(V)$(FLIPS) --create --bps F3DEX3/f3dzex2.code F3DEX3/F3DEX3_BrW_PA.code F3DEX3/F3DEX3_BrW_PA.code.bps
-	$(V)$(FLIPS) --create --bps F3DEX3/f3dzex2.data F3DEX3/F3DEX3_BrW_PA.data F3DEX3/F3DEX3_BrW_PA.data.bps
-	$(V)$(FLIPS) --create --bps F3DEX3/f3dzex2.code F3DEX3/F3DEX3_BrW_PB.code F3DEX3/F3DEX3_BrW_PB.code.bps
-	$(V)$(FLIPS) --create --bps F3DEX3/f3dzex2.data F3DEX3/F3DEX3_BrW_PB.data F3DEX3/F3DEX3_BrW_PB.data.bps
-	$(V)$(FLIPS) --create --bps F3DEX3/f3dzex2.code F3DEX3/F3DEX3_BrW_PC.code F3DEX3/F3DEX3_BrW_PC.code.bps
-	$(V)$(FLIPS) --create --bps F3DEX3/f3dzex2.data F3DEX3/F3DEX3_BrW_PC.data F3DEX3/F3DEX3_BrW_PC.data.bps
-	$(V)$(FLIPS) --create --bps F3DEX3/f3dzex2.code F3DEX3/F3DEX3_BrW_NOC.code F3DEX3/F3DEX3_BrW_NOC.code.bps
-	$(V)$(FLIPS) --create --bps F3DEX3/f3dzex2.data F3DEX3/F3DEX3_BrW_NOC.data F3DEX3/F3DEX3_BrW_NOC.data.bps
-	$(V)$(FLIPS) --create --bps F3DEX3/f3dzex2.code F3DEX3/F3DEX3_BrW_NOC_PA.code F3DEX3/F3DEX3_BrW_NOC_PA.code.bps
-	$(V)$(FLIPS) --create --bps F3DEX3/f3dzex2.data F3DEX3/F3DEX3_BrW_NOC_PA.data F3DEX3/F3DEX3_BrW_NOC_PA.data.bps
-	$(V)$(FLIPS) --create --bps F3DEX3/f3dzex2.code F3DEX3/F3DEX3_BrW_NOC_PB.code F3DEX3/F3DEX3_BrW_NOC_PB.code.bps
-	$(V)$(FLIPS) --create --bps F3DEX3/f3dzex2.data F3DEX3/F3DEX3_BrW_NOC_PB.data F3DEX3/F3DEX3_BrW_NOC_PB.data.bps
-	$(V)$(FLIPS) --create --bps F3DEX3/f3dzex2.code F3DEX3/F3DEX3_BrW_NOC_PC.code F3DEX3/F3DEX3_BrW_NOC_PC.code.bps
-	$(V)$(FLIPS) --create --bps F3DEX3/f3dzex2.data F3DEX3/F3DEX3_BrW_NOC_PC.data F3DEX3/F3DEX3_BrW_NOC_PC.data.bps
-	$(call print,Success!)
-
-verify:
-	$(V)$(MAKE) clean
-	$(V)$(MAKE) rom
-	@md5sum $(ROM)
-
-.PHONY: all rom compress clean assetclean distclean venv setup run wad iso patch create_f3dex3_patches verify
-
+.PHONY: all rom compress clean assetclean distclean venv setup run
 .DEFAULT_GOAL := rom
 
 #### Various Recipes ####
@@ -676,11 +588,6 @@ $(BUILD_DIR)/undefined_syms.txt: undefined_syms.txt
 $(BUILD_DIR)/baserom/%.o: $(EXTRACTED_DIR)/baserom/%
 	$(call print,Wrapping binary to ELF:,$<,$@)
 	$(V)$(OBJCOPY) -I binary -O elf32-big $< $@
-	
-$(BUILD_DIR)/F3DEX3/%.o: F3DEX3/%
-	$(call print,Wrapping binary to ELF:,$<,$@)
-	$(V)mkdir -p $(BUILD_DIR)/F3DEX3
-	$(V)$(OBJCOPY) -I binary -O elf32-big $< $@
 
 $(BUILD_DIR)/data/%.o: data/%.s
 	$(call print,Assembling:,$<,$@)
@@ -793,20 +700,6 @@ $(BUILD_DIR)/assets/%.jpg.inc.c: assets/%.jpg
 $(BUILD_DIR)/assets/%.jpg.inc.c: $(EXTRACTED_DIR)/assets/%.jpg
 	$(V)$(ZAPD) bren -eh -i $< -o $@
 
-F3DEX3/f3dzex2.code:
-	$(V)$(PYTHON) tools/data_extractor.py --start 0xBCD0F0 --size 0x1630 --input $(BASEROM_DIR)/baserom-decompressed.z64 --output $@
-
-F3DEX3/f3dzex2.data:
-	$(V)$(PYTHON) tools/data_extractor.py --start 0xBCE720 --size 0x420 --input $(BASEROM_DIR)/baserom-decompressed.z64 --output $@
-
-F3DEX3/F3DEX3%.code: F3DEX3/F3DEX3%.code.bps F3DEX3/f3dzex2.code
-	$(V)$(FLIPS) --apply F3DEX3/F3DEX3$*.code.bps F3DEX3/f3dzex2.code $@
-	
-F3DEX3/F3DEX3%.data: F3DEX3/F3DEX3%.data.bps F3DEX3/f3dzex2.data
-	$(V)$(FLIPS) --apply F3DEX3/F3DEX3$*.data.bps F3DEX3/f3dzex2.data $@
-
-.PRECIOUS: $(UCODE_FILES)
-
 # Audio
 
 AUDIO_BUILD_DEBUG ?= 0
diff --git a/include/config/config_safeguards.h b/include/config/config_safeguards.h
index cdc7f38fb..780637ada 100644
--- a/include/config/config_safeguards.h
+++ b/include/config/config_safeguards.h
@@ -146,68 +146,10 @@
     #define ENABLE_F3DEX3 false
 #endif
 
-
-/**
- * Default settings if not using HackerOoT mode
-*/
-#if !ENABLE_HACKEROOT
-    #undef SKIP_N64_BOOT_LOGO
-    #undef BOOT_TO_SCENE
-    #undef BOOT_TO_SCENE_NEW_GAME_ONLY
-    #undef BOOT_TO_FILE_SELECT
-    #undef DISABLE_DEBUG_FEATURES
-    #undef SHOW_CS_INFOS
-    #undef SHOW_INPUT_DISPLAY
-    #undef SHOW_TIME_INFOS
-    #undef INCLUDE_TEST_SCENES
-    #undef ENABLE_NO_CLIP
-    #undef ENABLE_CS_CONTROL
-    #undef ENABLE_FRAMERATE_OPTIONS
-    #undef ENABLE_MAP_SELECT
-    #undef ENABLE_INV_EDITOR
-    #undef ENABLE_EVENT_EDITOR
-    #undef ENABLE_REG_EDITOR
-    #undef ENABLE_CAMERA_DEBUGGER
-    #undef ENABLE_AUDIO_DEBUGGER
-    #undef ENABLE_ACTOR_DEBUGGER
-    #undef ENABLE_MSG_DEBUGGER
-    #undef ENABLE_DEBUG_SAVE
-    #undef MAP_SELECT_ON_FILE_1
-    #undef ENABLE_MOTION_BLUR_DEBUG
-
-    #define SKIP_N64_BOOT_LOGO true
-    #define BOOT_TO_SCENE false
-    #define BOOT_TO_SCENE_NEW_GAME_ONLY false
-    #define BOOT_TO_FILE_SELECT false
-    #define DISABLE_DEBUG_FEATURES false
-    #define SHOW_CS_INFOS false
-    #define SHOW_INPUT_DISPLAY false
-    #define SHOW_TIME_INFOS false
-    #define INCLUDE_TEST_SCENES true
-    #define ENABLE_NO_CLIP false
-    #define ENABLE_CS_CONTROL false
-    #define ENABLE_FRAMERATE_OPTIONS false
-    #define ENABLE_MAP_SELECT true
-    #define ENABLE_INV_EDITOR false
-    #define ENABLE_EVENT_EDITOR false
-    #define ENABLE_REG_EDITOR false
-    #define ENABLE_CAMERA_DEBUGGER true
-    #define ENABLE_AUDIO_DEBUGGER false
-    #define ENABLE_ACTOR_DEBUGGER false
-    #define ENABLE_MSG_DEBUGGER false
-    #define ENABLE_DEBUG_SAVE false
-    #define MAP_SELECT_ON_FILE_1 true
-    #define ENABLE_MOTION_BLUR_DEBUG false
-#endif
-
 /**
  * Used in if statements
 */
-#if ENABLE_HACKEROOT
 #define IS_DEBUG (OOT_DEBUG && !DISABLE_DEBUG_FEATURES)
-#else
-#define IS_DEBUG OOT_DEBUG
-#endif
 
 #if ENABLE_PROFILER && !ENABLE_HACKER_DEBUG
 #error "ENABLE_PROFILER requires ENABLE_HACKER_DEBUG"
@@ -216,7 +158,7 @@
 /**
  * Game
 */
-#define IS_MOTION_BLUR_ENABLED (ENABLE_HACKEROOT && ENABLE_MOTION_BLUR)
+#define IS_MOTION_BLUR_ENABLED (ENABLE_MOTION_BLUR)
 
 /**
  * Debug
diff --git a/spec b/spec
index adcb297a7..7af1d2fa6 100644
--- a/spec
+++ b/spec
@@ -19644,106 +19644,6 @@ beginseg
 endseg
 #endif
 
-#if !ENABLE_HACKEROOT
-beginseg
-    name "bump_texture_static"
-    compress
-    romalign 0x1000
-    include "$(BUILD_DIR)/baserom/bump_texture_static.o"
-endseg
-
-beginseg
-    name "anime_model_1_static"
-    compress
-    romalign 0x1000
-    include "$(BUILD_DIR)/baserom/anime_model_1_static.o"
-endseg
-
-beginseg
-    name "anime_model_2_static"
-    compress
-    romalign 0x1000
-    include "$(BUILD_DIR)/baserom/anime_model_2_static.o"
-endseg
-
-beginseg
-    name "anime_model_3_static"
-    compress
-    romalign 0x1000
-    include "$(BUILD_DIR)/baserom/anime_model_3_static.o"
-endseg
-
-beginseg
-    name "anime_model_4_static"
-    compress
-    romalign 0x1000
-    include "$(BUILD_DIR)/baserom/anime_model_4_static.o"
-endseg
-
-beginseg
-    name "anime_model_5_static"
-    compress
-    romalign 0x1000
-    include "$(BUILD_DIR)/baserom/anime_model_5_static.o"
-endseg
-
-beginseg
-    name "anime_model_6_static"
-    compress
-    romalign 0x1000
-    include "$(BUILD_DIR)/baserom/anime_model_6_static.o"
-endseg
-
-beginseg
-    name "anime_texture_1_static"
-    compress
-    romalign 0x1000
-    include "$(BUILD_DIR)/baserom/anime_texture_1_static.o"
-endseg
-
-beginseg
-    name "anime_texture_2_static"
-    compress
-    romalign 0x1000
-    include "$(BUILD_DIR)/baserom/anime_texture_2_static.o"
-endseg
-
-beginseg
-    name "anime_texture_3_static"
-    compress
-    romalign 0x1000
-    include "$(BUILD_DIR)/baserom/anime_texture_3_static.o"
-endseg
-
-beginseg
-    name "anime_texture_4_static"
-    compress
-    romalign 0x1000
-    include "$(BUILD_DIR)/baserom/anime_texture_4_static.o"
-endseg
-
-beginseg
-    name "anime_texture_5_static"
-    compress
-    romalign 0x1000
-    include "$(BUILD_DIR)/baserom/anime_texture_5_static.o"
-endseg
-
-beginseg
-    name "anime_texture_6_static"
-    compress
-    romalign 0x1000
-    include "$(BUILD_DIR)/baserom/anime_texture_6_static.o"
-endseg
-
-beginseg
-    name "softsprite_matrix_static"
-    compress
-    romalign 0x1000
-    include "$(BUILD_DIR)/baserom/softsprite_matrix_static.o"
-endseg
-#endif
-
 #if INCLUDE_EXAMPLE_SCENE
 beginseg
     name "example_scene"
diff --git a/src/code/z_scene.c b/src/code/z_scene.c
index 949e4c9d7..72cad51d0 100644
--- a/src/code/z_scene.c
+++ b/src/code/z_scene.c
@@ -62,27 +62,8 @@ void Object_InitContext(PlayState* play, ObjectContext* objectCtx) {
     u32 spaceSize;
     s32 i;
 
-#if ENABLE_HACKEROOT
+    // HackerOoT change: set a fixed allocation for the object heap
     spaceSize = OBJECT_BANK_SIZE;
-#else
-    if (play2->sceneId == SCENE_HYRULE_FIELD) {
-        spaceSize = 1000 * 1024 - OBJECT_SPACE_ADJUSTMENT;
-    } else if (play2->sceneId == SCENE_GANON_BOSS) {
-        if (gSaveContext.sceneLayer != 4) {
-            spaceSize = 1150 * 1024 - OBJECT_SPACE_ADJUSTMENT;
-        } else {
-            spaceSize = 1000 * 1024 - OBJECT_SPACE_ADJUSTMENT;
-        }
-    } else if (play2->sceneId == SCENE_SPIRIT_TEMPLE_BOSS) {
-        spaceSize = 1050 * 1024 - OBJECT_SPACE_ADJUSTMENT;
-    } else if (play2->sceneId == SCENE_CHAMBER_OF_THE_SAGES) {
-        spaceSize = 1050 * 1024 - OBJECT_SPACE_ADJUSTMENT;
-    } else if (play2->sceneId == SCENE_GANONDORF_BOSS) {
-        spaceSize = 1050 * 1024 - OBJECT_SPACE_ADJUSTMENT;
-    } else {
-        spaceSize = 1000 * 1024 - OBJECT_SPACE_ADJUSTMENT;
-    }
-#endif
 
     objectCtx->numEntries = objectCtx->numPersistentEntries = 0;
     objectCtx->mainKeepSlot = objectCtx->subKeepSlot = 0;
diff --git a/tools/data_extractor.py b/tools/data_extractor.py
deleted file mode 100644
index 997ad52a6..000000000
--- a/tools/data_extractor.py
+++ /dev/null
@@ -1,61 +0,0 @@
-#!/usr/bin/python3
-
-import argparse
-
-
-def extract(start: int, size: int, input: str, output: str):
-    """Extracts ``size`` bytes from ``input``, at offset ``start``, and writes it to ``output``
-
-    Parameters:
-    - ``start``: int, defines where to start reading the file
-    - ``size``: int, how many bytes to read from the file
-    - ``input``: str, path to the file to read
-    - ``output``: str, path to the file to write
-    """
-
-    with open(input, "rb") as file:
-        file.seek(start)
-        data = file.read(size)
-
-    with open(output, "wb") as file:
-        file.write(data)
-
-
-def main():
-    parser = argparse.ArgumentParser(description="Extracts data from a file for HackerOoT.")
-
-    parser.add_argument(
-        "--start",
-        dest="start",
-        help="Offset to the data (uses hex)",
-        required=True,
-    )
-
-    parser.add_argument(
-        "--size",
-        dest="size",
-        help="How much to read (uses hex)",
-        required=True,
-    )
-
-    parser.add_argument(
-        "--input",
-        dest="input",
-        help="Input file",
-        required=True,
-    )
-
-    parser.add_argument(
-        "--output",
-        dest="output",
-        help="Output file",
-        required=True,
-    )
-
-    args = parser.parse_args()
-    extract(int(args.start, 16), int(args.size, 16), args.input, args.output)
-    print("Data extracted successfully!")
-
-
-if __name__ == "__main__":
-    main()