TWLoader has been discontinued. Please use DSiMenu++.
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Old post

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TWLoader is a CTR-mode GUI that looks and feels like the Nintendo DSi Menu (theme can be changed to R4 or akmenu/Wood).
It is a frontend for nds-bootstrap, the SD ROM loader, and also a frontend for flashcards.
It can also serve as a replacement for flashcard menus.
With this, you can run your NDS games, with an enhanced 240p/3D-visual version of the DS/DSi boot screen, clock speed of 133mhz (faster than normal DS), and higher sound quality.

Video by @Nomelas


You can also change the UI color to your favorite color, and have glowing rainbow colors in the Notification LED.

Is this an emulator, you may ask? No. NDS/DSi games are ran natively in TWL_FIRM.

Table of contents

1. Instructions
2. Custom box art instructions
3. Controls
4. List of DS games that work from SD Card
   
5. Todo
6. Credits
7. FAQs

(Always updated)
Scan these QR Codes:

GUI (1 code)

TWL-NAND SIDE (2 codes)

and Download here. (CIA files are in "sdmc:/_nds/twloader/cia/", if you skipped QR downloading.)
NOTE: The 3DSX version only works with Rosalina functionality, so it doesn't work via payloads.
NOTE2: The 3DSX demo version does not launch games, due to it being impossible with payloads.

Music files
Put "music.wav" at "sdmc:/_nds/twloader/".
Music must be 44khz, and 1 minute.

Instructions

1. Extract the files/folders in the "sdroot" folder to the 3DS' SD Card root. Do not extract the "sdroot" folder itself to the SD Card root.
2. Put .nds ROMs in "sdmc:/roms/nds/" (and .gb/.sgb/.gbc ROMs in "sdmc:/roms/gb/"). Create the folders if they don't exist.
3. Put a Mario Kart DS ROM at "sdmc:/roms/nds/".
4. Open TWLoader.
5. Press SELECT on MKDS.
6. Select "Set as donor ROM". This will make some games that can't save, be able to save.
7. v5.2.1 or below only: Dump the DSP firm, as that's needed to play the sound effects and music.
   Check here: https://gbatemp.net/threads/release-dsp-dump.423860/

IMPORTANT NOTE: If you plan on do a system transfer, before you do it, uninstall both parts of the TWLNAND side app first, unless you want to keep using TWLoader on the system that had it's stuff transferred to the new system.

(Optional) Run ROMs from your Slot-1 flashcard

Download a pack for your flashcard:
DSTT/R4i Gold/R4i-SDHC/R4 SDHC Upgrade/SC DSONE (not needed as of v5.0.0, as the one for TWLoader is in TWLoader.7z.)
Original R4/M3 Simply (unknown version broke support)
R4iDSN/R4i Gold RTS/R4 Ultra (v5.1.0 broke support for "Add Games" and added games, but R4 Ultra works.)
Galaxy Eagle/M3DS Real
Acekard RPG
Ace 3DS+/Gateway Blue Card/R4iLS/R4iTT (Saving does not work.)
SuperCard DSTWO

NOTE: If you want to use Acekard 2i, use SRLoader instead.

Extract what's in "for Slot-1 microSD" to the root of the flashcard's microSD card.

In TWLoader.7z, extract the files/folders in the "flashcardsdroot (all)" and "flashcardsdroot (flashcardnamehere)" folders to the flashcard's microSD card root. Do not extract the "flashcardsdroot (all)" or "flashcardsdroot (flashcardnamehere)" folders themselves to the microSD card root.

To add a game from the flashcard:

1. Launch the "Add Games" menu.
2. Select a .nds file.
3. The banner and .ini files will be created, and your game will show up in TWLoader.

To launch your game on the flashcard:

1. Open TWLoader, and press START while on the DSi Menu theme.
2. Press A on game location, and it will switch to flashcard.
3. Go to Settings.
4. Press R three times to go to NTR/TWL settings.
5. In NTR/TWL settings, select "Flashcard(s) select".
6. Pick your flashcard.
7. Out of Settings, select your game, and the ROM should load.

Custom box art instructions

1. Create your .png file that's 128x115.
2. Name the .png file to the same filename as the game, but with ".png" added to the end (ex. SD card: game.nds.png, Flashcard: game.ini.png).
3. Save it to "sdmc:/_nds/twloader/boxart/" for games on the SD card, "sdmc:/_nds/twloader/boxart/flashcard/" for games on the Slot-1 flashcard, sdmc:/_nds/twloader/boxart/slot1/" for Slot-1 games, or "sdmc:/_nds/twloader/boxart/gb/" for GameBoy/Super GameBoy/GameBoy Color games.

DSi Menu theme: ROM select controls

• Left/Right / Touch left/right game icons: Select a game/app.
• L: Previous page.
• R: Next page.
• Y: Change icon size.
• A / Touch selected icon: Launch selected game/app.
• START: Start menu.
• SELECT: Game settings.

Game settings selections

1. ARM9 CPU Speed
2. Use set donor ROM
3. Set as donor ROM: Applies an ARM7 binary from the set ROM, to the game you're running with non-working saves.
4. Set LED color: A set color will appear in the Notification LED.

R4 theme: menu controls

• Left/Right: Move cursor.
• A: Enter selected icon.
• SELECT: Open Settings.

R4 theme: ROM select controls

• Up: Move up.
• Down: Move down.
• Left: Move up 10.
• Right: Move down 10.
• L: Switch game location.
  
• A: Start game.
• B: Back to menu.

Wood theme controls

• Up/Down: Move cursor.
• A: Enter selection.

Settings controls
Settings will be saved on app exit or game/app launch.

• L: Previous page.
• R: Next page.
• Y/A: Change selected setting.
• B: Go back to ROM select screen.

DS ROM play controls
NOTE: Only for DSTT, R4i Gold, R4i-SDHC, SC DSONE users.

• L+R+A+B+X+Y: Bring up the 3DS error screen, as rebooting into SRLoader hasn't been implemented yet.

For SD card users:

• L+R+DOWN+B: Reboot into SRLoader.

Please check this list:
List of DS games that work from SD Card


Todo (ranging from high to low)

• Add multisaving support for DS games.
• Add cheat menu.
• Load themes stored on SD Card.

Credits

• @ahezard: Loading banner icons from .nds files.
• @Billy Acuña: Old TWLoader logo.
  
• @Joom: New and current TWLoader logo.
• @cheuble: Sound engine.
• @Gericom: GBARunner2.
• @Drenn: GameYob.
• @MarcusD: Code for glowing rainbow colors in Notification LED.

This wouldn't have been possible without the following.

• @ahezard: nds-bootstrap, for SD ROM loading.
• @Apache Thunder: NTR-Launcher, for NTR Slot-1 game loading, and the recreation of the DS/DSi boot screens (prior to v5.1.0).
• @shutterbug2000: File browsing code.
• @spinal_cord: DSi4DS graphic files.

FAQs,

look here.

Q: Is TWLoader a DS/DSi emulator?
A: No. TWLoader is not an emulator (as stated above). When you launch a game in TWLoader, the system reboots into TWL mode, then switch to NTR mode for running your selected DS game (via the backend nds-bootstrap, if ROM is on SD card).

Q: Why is TWLoader taking me back to HOME Menu after updating itself?
A: Some versions of TWLoader have a bug where it always updates itself to the latest version, even if it's already on the latest version.
To fix this, either turn off Wifi and turn off auto-update TWLoader in the settings screen, or open settings.ini, and set AUTODOWNLOAD (in [FRONTEND]) to 0.

Q: What's the TWLNAND side CIA? Does it patch TWL_FIRM?
A: No. It's a DSiWare apps only used by the GUI (not seen in HOME Menu). The TWLNAND side starts bootstrap for running the ROMs and certain flashcards, and part 2 runs Slot-1 games/flashcards.

Q: Why do I get a white screen when trying to load a game from DSTT, Original R4, or the Acekard RPG?
A: A white screen will happen sometimes. Just try again if it happens.

Q: Why do I get a white screen when trying to load a game from SD Card?
A: Please note that not all games work from SD Card yet. Check the list above.
If it's listed as compatible, try again. Also, make sure your SD card is formatted to FAT32 with 32kb cluster size.

Q: How do I run a game in GBARunner2?
A: Put your SRAM-patched GBA ROM in the SD card, and put the BIOS in the SD root as "bios.bin".
To SRAM-patch your ROM, use GBATA.

Q: Why is there lagging when picking a game?
A: The previous/next boxart and icon images are loaded, instead of them being loaded all at once. This is done to prevent memory leaks.

Q: Won't the LED feature cause an MCU brick?
A: Don't worry. @MarcusD said that you can only MCU brick on firmwares 8.1 or below.
It's confirmed there aren't any bricks above 8.1.

Q: Why am I'm getting the error screen when launching a game?
A1: Make sure you're using an up-to-date CFW, namely Luma3DS.
A2: Make sure part 1 & 2 of TWLNAND side is installed to both SysNAND and EmuNAND.

Q: Why do I get a black screen when launching a game, or "Add Games"?
A: TWL_FIRM may be broken somehow. Please follow this part of the guide.
If you're using a boot manager to boot Luma, such as BootAnim9, look here.

Q: Why do I get an auto-shutdown when launching a game, or "Add Games"?
A: It's due to a pre-patched TWL_FIRM still being installed. Please follow this part of the guide.
If you're using a boot manager to boot Luma, such as BootAnim9, look here.

Q: Will there be a way to return to the TWLoader menu while playing a game?
A: May require a new feature to be added for Luma.

Q: How do I update TWLoader on the 3DS?
A: To manually update, select "Update TWLoader" in TWLoader settings.

Q: I'm getting a bootstrap not found error?
A1: In settings screen, try updating the bootstraps.
A2: If you get that message when trying to run homebrew, get "hb-bootstrap.nds" from TWLoader.7z, and place it in "sd:/_nds".