Pluto does not contain a built-in asset extractor and must be compiled from source code, like many other SM64 PC ports.
You will need to obtain an unmodified, vanilla US ROM of Super Mario 64.
Download and install the latest version of MSYS2.
Launch the MINGW64 executable (MINGW32/32-bit is untested). If you can’t find it, search MINGW in the start menu and select the app with the blue icon.
Enter pacman -Syuu in the prompt and hit enter. Press Y whenever it asks you to update packages.
Next run this command in the terminal to install our necessary packages:
pacman -S unzip make git mingw-w64-i686-gcc mingw-w64-x86_64-gcc mingw-w64-i686-glew mingw-w64-x86_64-glew mingw-w64-i686-SDL2 mingw-w64-i686-SDL mingw-w64-x86_64-SDL2 mingw-w64-x86_64-SDL python3
Clone the source code and enter its folder:
git clone https://github.com/Llennpie/Pluto && cd Pluto
Next, run explorer . to open a new File Explorer window at Pluto’s root directory. Drop your ROM in here and rename it to baserom.us.z64.
Begin compiling:
make
(You can optionally run make -j for a faster compile but at the cost of CPU usage.)
When completed, an executable will be created in Pluto\build\us_pc\.